2022-05-11 REL PDBj PDBj PDBj 2022-01-12 2022-03-30 2022-03-30 2022-05-11 Japan Agency for Medical Research and Development (AMED) JP21am0101071 Japan Cryo-EM structure of GH31 alpha-1,3-glucosidase from Lactococcus lactis subsp. cremoris Ikegaya M Moriya T Adachi N Kawasaki M Park EY Miyazaki T Ikegaya M Moriya T Adachi N Kawasaki M Park EY Miyazaki T Structural basis of the strict specificity of a bacterial GH31 alpha-1,3-glucosidase for nigerooligosaccharides. J.Biol.Chem. US 298 101827 101827 2022 35293315 doi:10.1016/j.jbc.2022.101827 1083-351X 0071 JBCHA3 EMD-32571 associated EM volume LlGH31_u1 hexamer LlGH31_u1 hexamer 0 1
homo hexamer
Lactococcus lactis subsp. cremoris MG1363 Escherichia coli BL21(DE3) BL21(DE3) pET28a 0.516 LlGH31_u1 Lactococcus lactis subsp. cremoris MG1363 MG1363 Escherichia coli BL21(DE3) LEVO MGSSHHHHHHSSGLVPRGSHMVSELESKYMNNNIIKFDKARFTVLTEHLIRIEYSETGEFEERMTQMVQNREFSEVNFDIIEKEETIEIITSTVHLYYNGGEFTNASLFADVKFNFSVYSNRWYFGEKSDGNLKGTTRTLDMIDGECPLEDGIMSKNGFAVLADKGKVLTEVGDIAGNSVSTIDLYLFAYGRDYRQALKDFYQLTGNTPKLPRFALGNWWSRYYDYSDKSYLALMDKFTDKKVPLSVSVIDMDWHKVSEVPSRFGSGWTGYSWNKKLFPNPENFIDELHQRKLKVTLNDHPADGIRAFEDPYPQVAQTLDLNTELEEAAKFDFDNLKFRKAYFEEVHGPLEKEGVDFWWIDWQQGAISKSGVDPLWLLNHYQYQNAQKKHKNNIILSRYAGPGSHRYPLGFSGDSVISWASLDFQPYFTSTASNIGYTWWSHDIGGHMQGYKDAELSLRWLQFGVFSPINRLHSSKSEFTSKEPWHFDAVIEQSMIDFLQLRHQLIPYLYSANLITASEGRALVEPLYYEYPMEEEAYQHRNQYLFGEQLMVAPITEKMNSLLQMGSVEVWFPEGTWYDFFSGQPYDGKVSLKVYREITEMPVFAKAGAIIPLDKNPLKKEEIPSEIIWKIFPGADGEYLLLEEDNETKAEFVNGIFTVTSKKESSRKHTIIYGEHEIVSAKRGEFSIDLNGKEENFDWNFSTALFRRLDIAEISYEQKDEILQQLSLIEEHEKQVAFIKTNENQELQNSLFELLYSGK 3.2.1.84 singleParticle particle 0.58 7.0 300.0 NaCl sodium chloride 20.0 NaH2PO4 sodium dihydrogen phosphate Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE AIR
The grid was washed by acetone prior to use.
 ETHANE 100 291 FEI VITROBOT MARK IV
Blotting time was 5 seconds (blot force 15).
This sample was mono-disperse.
 TFS TALOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 0.8 2.0 120000.0 NITROGEN FEI FALCON III (4k x 4k) COUNTING 4096 4096 1 995 65.95 50.0 1 267294 Gctf 1.18 GCTF_v1.18_sm30-7a5_cu10.1
An ab initio model was generated using RELION3.1.2's own implementation of Stochastic Gradient Descent (SGD) algorithm and low-pass filtered to 30 A for use as an initial model for 3D classification.
 1 D3 FOURIER SPACE 2.73 FSC 0.143 CUT-OFF RELION 3.1.2 44606 MAXIMUM LIKELIHOOD RELION 3.1.2 MAXIMUM LIKELIHOOD RELION 3.1.2 2 31669.0 RELION 3.1.2 emd_32571.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 450.56 450.56 450.56 90.0 90.0 90.0 X Y Z -0.11023122 0.22144265 -0.00012851362 0.0056734174 0.88 0.88 0.88 0.05 AUTHOR emd_32571_msk_1.map emd_32571_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 450.56 450.56 450.56 90.0 90.0 90.0 X Y Z -0.031215085 0.1053989 -0.000132652 0.003149733 0.88 0.88 0.88 AUTHOR emd_32571_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 450.56 450.56 450.56 90.0 90.0 90.0 X Y Z -0.030123444 0.10671271 -0.00012437525 0.0031238855 0.88 0.88 0.88 AUTHOR