<emd emdb_id="EMD-3244" version="3.0.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
    <admin>
        <current_status>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2015-11-13</deposition>
            <header_release>2015-11-25</header_release>
            <map_release>2016-01-13</map_release>
            <update>2016-03-09</update>
        </key_dates>
        <title>Electron negative-staining microscopy of an aerolysin-like protein</title>
        <authors_list>
            <author>Jia N</author>
            <author>Liu N</author>
            <author>Cheng W</author>
            <author>Jiang YL</author>
            <author>Sun H</author>
            <author>Chen LL</author>
            <author>Peng JH</author>
            <author>Zhang YH</author>
            <author>Zhang ZH</author>
            <author>Wang XJ</author>
            <author>Cai G</author>
            <author>Wang JF</author>
            <author>Zhang ZY</author>
            <author>Wu H</author>
            <author>Wang HW</author>
            <author>Chen YX</author>
            <author>Zhou CZ</author>
        </authors_list>
        <keywords />
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Jia N</author>
                    <author order="2">Liu N</author>
                    <author order="3">Cheng W</author>
                    <author order="4">Jiang YL</author>
                    <author order="5">Sun H</author>
                    <author order="6">Chen LL</author>
                    <author order="7">Peng JH</author>
                    <author order="8">Zhang YH</author>
                    <author order="9">Zhang ZH</author>
                    <author order="10">Wang XJ</author>
                    <author order="11">Cai G</author>
                    <author order="12">Wang JF</author>
                    <author order="13">Zhang ZY</author>
                    <author order="14">Wu H</author>
                    <author order="15">Wang HW</author>
                    <author order="16">Chen YX</author>
                    <author order="17">Zhou CZ</author>
                    <title>Structural basis for receptor recognition and pore formation of a zebrafish aerolysin-like protein</title>
                    <journal>EMBO REP.</journal>
                    <volume>17</volume>
                    <first_page>235</first_page>
                    <last_page>248</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">26711430</external_references>
                    <external_references type="DOI">doi:10.15252/embr.201540851</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Dln1 (a zebrafish aerolysin-like protein) oligomer on phospholipid monolayer</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Dln1 (a zebrafish aerolysin-like protein) oligomer on phospholipid monolayer</name>
                <oligomeric_state>Octameric Dln1 reconstituted on lipid monolayer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.28</experimental>
                    <theoretical units="MDa">0.28</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Dln1</name>
                <natural_source database="NCBI">
                    <organism ncbi="7955">Danio rerio</organism>
                    <synonym_organism>zebrafish</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.28</experimental>
                    <theoretical units="MDa">0.28</theoretical>
                </molecular_weight>
                <number_of_copies>8</number_of_copies>
                <oligomeric_state>Octamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">Q5CZR5</external_references>
                </sequence>
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>electronCrystallography</method>
            <aggregation_state>twoDArray</aggregation_state>
            <specimen_preparation_list>
                <crystallography_preparation preparation_id="1">
                    <concentration units="mg/mL">0.2</concentration>
                    <buffer>
                        <ph>5.5</ph>
                        <details>50 mM MES, 150 mM NaC</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>Grids attached with two-dimensional protein crystal on
lipid monolayer were gently washed, followed by negative staining with 2%
w/v uranyl acetate for about 30 seconds.</details>
                    </staining>
                    <grid>
                        <details>200 mesh copper grid with thin holey carbon
support. The grids were not glow discharged.</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                    <details>Crystals grown on a lipid-monolayer</details>
                    <crystal_formation>
                        <details>Crystals grown on a lipid-monolayer</details>
                    </crystal_formation>
                </crystallography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <crystallography_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI 12</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_cs units="mm">6.7</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.588</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">1.5</nominal_defocus_max>
                    <nominal_magnification>98000.0</nominal_magnification>
                    <calibrated_magnification>98000.0</calibrated_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <date>2014-10-09</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <number_real_images>45</number_real_images>
                        </image_recording>
                    </image_recording_list>
                    <tilt_angle_min>0</tilt_angle_min>
                    <tilt_angle_max>40</tilt_angle_max>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">0</min_angle>
                            <max_angle units="deg">40</max_angle>
                        </axis1>
                    </tilt_series>
                </crystallography_microscopy>
            </microscopy_list>
            <crystallography_processing image_processing_id="1">
                <details>Images were unbent using 2dx.</details>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">20.0</resolution>
                    <resolution_method>DIFFRACTION PATTERN/LAYERLINES</resolution_method>
                    <software_list>
                        <software>
                            <name>2dx</name>
                        </software>
                    </software_list>
                </final_reconstruction>
                <crystal_parameters>
                    <unit_cell>
                        <a units="&#8491;">125</a>
                        <b units="&#8491;">125</b>
                        <gamma units="deg">90.0</gamma>
                        <alpha units="deg">90.0</alpha>
                        <beta units="deg">90.0</beta>
                    </unit_cell>
                    <plane_group>P 4</plane_group>
                </crystal_parameters>
            </crystallography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="32182">
        <file>emd_3244.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>207</col>
            <row>198</row>
            <sec>201</sec>
        </dimensions>
        <origin>
            <col>-60</col>
            <row>-55</row>
            <sec>-55</sec>
        </origin>
        <spacing>
            <x>198</x>
            <y>207</y>
            <z>201</z>
        </spacing>
        <cell>
            <a units="&#8491;">129.375</a>
            <b units="&#8491;">123.75</b>
            <c units="&#8491;">125.625</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-234.948883059999986</minimum>
            <maximum>250.0</maximum>
            <average>-0.78882813</average>
            <std>51.022731780000001</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">0.625</x>
            <y units="&#8491;">0.625</y>
            <z units="&#8491;">0.625</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>55.0</level>
                <source>EMDB</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of mutant aerolysin-like protein</annotation_details>
        <details>::::EMDATABANK.org::::EMD-3244::::</details>
    </map>
</emd>