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- PDB-8hcj: Structure of GH43 family enzyme, Xylan 1, 4 Beta- xylosidase from... -

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Basic information

Entry
Database: PDB / ID: 8hcj
TitleStructure of GH43 family enzyme, Xylan 1, 4 Beta- xylosidase from pseudopedobacter saltans
ComponentsXylan 1,4-beta-xylosidase
KeywordsHYDROLASE / GH43 family / Xylan / Xylosidase
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / polysaccharide catabolic process / carbohydrate binding
Similarity search - Function
Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Xylan 1,4-beta-xylosidase
Similarity search - Component
Biological speciesPseudopedobacter saltans DSM 12145 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.566 Å
AuthorsVishwakarma, P. / Sachdeva, E. / Goyal, A. / Ethayathulla, A.S. / Das, U. / Kaur, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: To Be Published
Title: Structure of GH43 family enzyme, Xylan 1, 4 Beta- xylosidase from pseudopedobacter saltans
Authors: Vishwakarma, P. / Kaur, P. / Sachdeva, E. / Ethayathulla, A.S. / Das, U. / Goyal, A.
History
DepositionNov 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Xylan 1,4-beta-xylosidase
E: Xylan 1,4-beta-xylosidase
H: Xylan 1,4-beta-xylosidase
A: Xylan 1,4-beta-xylosidase
B: Xylan 1,4-beta-xylosidase
G: Xylan 1,4-beta-xylosidase
C: Xylan 1,4-beta-xylosidase
F: Xylan 1,4-beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)407,14524
Polymers406,5048
Non-polymers64116
Water23,8701325
1
D: Xylan 1,4-beta-xylosidase
A: Xylan 1,4-beta-xylosidase
B: Xylan 1,4-beta-xylosidase
C: Xylan 1,4-beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,57312
Polymers203,2524
Non-polymers3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Xylan 1,4-beta-xylosidase
H: Xylan 1,4-beta-xylosidase
G: Xylan 1,4-beta-xylosidase
F: Xylan 1,4-beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,57312
Polymers203,2524
Non-polymers3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.340, 89.662, 138.437
Angle α, β, γ (deg.)102.734, 93.985, 98.237
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21D
32D
42D
53D
63D
74D
84D
95D
105D
116D
126D
137D
147D
158D
168D
179D
189D
1910D
2010D
2111D
2211D
2312D
2412D
2513D
2613D
2714D
2814D
2915D
3015D
3116D
3216D
3317D
3417D
3518D
3618D
3719D
3819D
3920D
4020D
4121D
4221D
4322D
4422D
4523D
4623D
4724D
4824D
4925D
5025D
5126D
5226D
5327D
5427D
5528D
5628D

NCS domain segments:

Auth asym-ID: D / Label asym-ID: A

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111METMETLYSLYS21 - 45321 - 453
211METMETLYSLYS21 - 45321 - 453
322METMETLYSLYS21 - 45321 - 453
422METMETLYSLYS21 - 45321 - 453
533METMETLYSLYS21 - 45321 - 453
633METMETLYSLYS21 - 45321 - 453
744METMETLYSLYS21 - 45321 - 453
844METMETLYSLYS21 - 45321 - 453
955GLNGLNSERSER22 - 45222 - 452
1055GLNGLNSERSER22 - 45222 - 452
1166GLNGLNSERSER22 - 45222 - 452
1266GLNGLNSERSER22 - 45222 - 452
1377GLNGLNSERSER22 - 45222 - 452
1477GLNGLNSERSER22 - 45222 - 452
1588METMETLYSLYS21 - 45321 - 453
1688METMETLYSLYS21 - 45321 - 453
1799METMETLYSLYS21 - 45321 - 453
1899METMETLYSLYS21 - 45321 - 453
191010METMETLYSLYS21 - 45321 - 453
201010METMETLYSLYS21 - 45321 - 453
211111GLNGLNSERSER22 - 45222 - 452
221111GLNGLNSERSER22 - 45222 - 452
231212GLNGLNSERSER22 - 45222 - 452
241212GLNGLNSERSER22 - 45222 - 452
251313GLNGLNSERSER22 - 45222 - 452
261313GLNGLNSERSER22 - 45222 - 452
271414METMETLYSLYS21 - 45321 - 453
281414METMETLYSLYS21 - 45321 - 453
291515METMETLYSLYS21 - 45321 - 453
301515METMETLYSLYS21 - 45321 - 453
311616GLNGLNSERSER22 - 45222 - 452
321616GLNGLNSERSER22 - 45222 - 452
331717GLNGLNSERSER22 - 45222 - 452
341717GLNGLNSERSER22 - 45222 - 452
351818GLNGLNSERSER22 - 45222 - 452
361818GLNGLNSERSER22 - 45222 - 452
371919METMETLYSLYS21 - 45321 - 453
381919METMETLYSLYS21 - 45321 - 453
392020GLNGLNSERSER22 - 45222 - 452
402020GLNGLNSERSER22 - 45222 - 452
412121GLNGLNSERSER22 - 45222 - 452
422121GLNGLNSERSER22 - 45222 - 452
432222GLNGLNSERSER22 - 45222 - 452
442222GLNGLNSERSER22 - 45222 - 452
452323GLNGLNSERSER22 - 45222 - 452
462323GLNGLNSERSER22 - 45222 - 452
472424GLNGLNSERSER22 - 45222 - 452
482424GLNGLNSERSER22 - 45222 - 452
492525GLNGLNSERSER22 - 45222 - 452
502525GLNGLNSERSER22 - 45222 - 452
512626GLNGLNLYSLYS22 - 45322 - 453
522626GLNGLNLYSLYS22 - 45322 - 453
532727GLNGLNLYSLYS22 - 45322 - 453
542727GLNGLNLYSLYS22 - 45322 - 453
552828GLNGLNLYSLYS22 - 45322 - 453
562828GLNGLNLYSLYS22 - 45322 - 453

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56

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Components

#1: Protein
Xylan 1,4-beta-xylosidase


Mass: 50813.023 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudopedobacter saltans DSM 12145 (bacteria)
Strain: ATCC 51119 / DSM 12145 / JCM 21818 / CCUG 39354 / LMG 10337 / NBRC 100064 / NCIMB 13643
Gene: Pedsa_2569 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: F0S5E9, xylan 1,4-beta-xylosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 18% PEG 3350, 5% PROPANOL, 0.15M IMIDAZOLE

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.5→134.29 Å / Num. obs: 103346 / % possible obs: 95 % / Redundancy: 1.92 % / Biso Wilson estimate: 30.2 Å2 / CC1/2: 0.94 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.07 / Rrim(I) all: 0.1 / Net I/σ(I): 0.04
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.01 % / Rmerge(I) obs: 0.02 / Num. unique obs: 5300 / CC1/2: 0.93 / Rpim(I) all: 0.19 / Rrim(I) all: 0.28 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Cootmodel building
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NOV
Resolution: 2.566→134.29 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.182 / SU B: 10.212 / SU ML: 0.218 / Average fsc free: 0.9701 / Average fsc work: 0.9826 / Cross valid method: FREE R-VALUE / ESU R Free: 0.3 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2091 5180 5.012 %
Rwork0.1634 98163 -
all0.166 --
obs-103343 95.375 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.093 Å2
Baniso -1Baniso -2Baniso -3
1-2.558 Å21.763 Å20.582 Å2
2---0.804 Å20.843 Å2
3----2.466 Å2
Refinement stepCycle: LAST / Resolution: 2.566→134.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27430 0 16 1325 28771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01128254
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.64838367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80853453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.871588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.327104503
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.669101311
X-RAY DIFFRACTIONr_chiral_restr0.0860.23925
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0221888
X-RAY DIFFRACTIONr_nbd_refined0.2060.212632
X-RAY DIFFRACTIONr_nbtor_refined0.3190.219274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.21490
X-RAY DIFFRACTIONr_metal_ion_refined0.1810.243
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.213
X-RAY DIFFRACTIONr_mcbond_it4.5193.22513836
X-RAY DIFFRACTIONr_mcangle_it6.3844.82417281
X-RAY DIFFRACTIONr_scbond_it5.7913.35814418
X-RAY DIFFRACTIONr_scangle_it7.7454.91121086
X-RAY DIFFRACTIONr_lrange_it10.50661.295122532
X-RAY DIFFRACTIONr_ncsr_local_group_10.1180.0514111
X-RAY DIFFRACTIONr_ncsr_local_group_20.120.0514096
X-RAY DIFFRACTIONr_ncsr_local_group_30.1210.0514029
X-RAY DIFFRACTIONr_ncsr_local_group_40.1210.0514019
X-RAY DIFFRACTIONr_ncsr_local_group_50.1210.0513867
X-RAY DIFFRACTIONr_ncsr_local_group_60.1230.0514048
X-RAY DIFFRACTIONr_ncsr_local_group_70.120.0514008
X-RAY DIFFRACTIONr_ncsr_local_group_80.1110.0514208
X-RAY DIFFRACTIONr_ncsr_local_group_90.1230.0513967
X-RAY DIFFRACTIONr_ncsr_local_group_100.1180.0514040
X-RAY DIFFRACTIONr_ncsr_local_group_110.1220.0513920
X-RAY DIFFRACTIONr_ncsr_local_group_120.1180.0514054
X-RAY DIFFRACTIONr_ncsr_local_group_130.1240.0513952
X-RAY DIFFRACTIONr_ncsr_local_group_140.1240.0514016
X-RAY DIFFRACTIONr_ncsr_local_group_150.1150.0514113
X-RAY DIFFRACTIONr_ncsr_local_group_160.120.0513911
X-RAY DIFFRACTIONr_ncsr_local_group_170.1130.0514157
X-RAY DIFFRACTIONr_ncsr_local_group_180.1260.0514011
X-RAY DIFFRACTIONr_ncsr_local_group_190.1230.0514020
X-RAY DIFFRACTIONr_ncsr_local_group_200.1240.0513847
X-RAY DIFFRACTIONr_ncsr_local_group_210.1230.0513959
X-RAY DIFFRACTIONr_ncsr_local_group_220.1240.0513978
X-RAY DIFFRACTIONr_ncsr_local_group_230.1260.0513889
X-RAY DIFFRACTIONr_ncsr_local_group_240.1180.0514037
X-RAY DIFFRACTIONr_ncsr_local_group_250.1240.0514026
X-RAY DIFFRACTIONr_ncsr_local_group_260.1230.0513932
X-RAY DIFFRACTIONr_ncsr_local_group_270.1250.0513921
X-RAY DIFFRACTIONr_ncsr_local_group_280.1230.0514067
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11DX-RAY DIFFRACTIONLocal ncs0.117920.05008
12DX-RAY DIFFRACTIONLocal ncs0.117920.05008
23DX-RAY DIFFRACTIONLocal ncs0.120340.05008
24DX-RAY DIFFRACTIONLocal ncs0.120340.05008
35DX-RAY DIFFRACTIONLocal ncs0.121450.05008
36DX-RAY DIFFRACTIONLocal ncs0.121450.05008
47DX-RAY DIFFRACTIONLocal ncs0.121450.05008
48DX-RAY DIFFRACTIONLocal ncs0.121450.05008
59DX-RAY DIFFRACTIONLocal ncs0.120990.05008
510DX-RAY DIFFRACTIONLocal ncs0.120990.05008
611DX-RAY DIFFRACTIONLocal ncs0.122740.05008
612DX-RAY DIFFRACTIONLocal ncs0.122740.05008
713DX-RAY DIFFRACTIONLocal ncs0.119840.05009
714DX-RAY DIFFRACTIONLocal ncs0.119840.05009
815DX-RAY DIFFRACTIONLocal ncs0.110970.05009
816DX-RAY DIFFRACTIONLocal ncs0.110970.05009
917DX-RAY DIFFRACTIONLocal ncs0.123410.05008
918DX-RAY DIFFRACTIONLocal ncs0.123410.05008
1019DX-RAY DIFFRACTIONLocal ncs0.117980.05008
1020DX-RAY DIFFRACTIONLocal ncs0.117980.05008
1121DX-RAY DIFFRACTIONLocal ncs0.121770.05008
1122DX-RAY DIFFRACTIONLocal ncs0.121770.05008
1223DX-RAY DIFFRACTIONLocal ncs0.118360.05008
1224DX-RAY DIFFRACTIONLocal ncs0.118360.05008
1325DX-RAY DIFFRACTIONLocal ncs0.123850.05008
1326DX-RAY DIFFRACTIONLocal ncs0.123850.05008
1427DX-RAY DIFFRACTIONLocal ncs0.124190.05008
1428DX-RAY DIFFRACTIONLocal ncs0.124190.05008
1529DX-RAY DIFFRACTIONLocal ncs0.114930.05008
1530DX-RAY DIFFRACTIONLocal ncs0.114930.05008
1631DX-RAY DIFFRACTIONLocal ncs0.120140.05008
1632DX-RAY DIFFRACTIONLocal ncs0.120140.05008
1733DX-RAY DIFFRACTIONLocal ncs0.112610.05009
1734DX-RAY DIFFRACTIONLocal ncs0.112610.05009
1835DX-RAY DIFFRACTIONLocal ncs0.126220.05008
1836DX-RAY DIFFRACTIONLocal ncs0.126220.05008
1937DX-RAY DIFFRACTIONLocal ncs0.122980.05008
1938DX-RAY DIFFRACTIONLocal ncs0.122980.05008
2039DX-RAY DIFFRACTIONLocal ncs0.123530.05008
2040DX-RAY DIFFRACTIONLocal ncs0.123530.05008
2141DX-RAY DIFFRACTIONLocal ncs0.122850.05008
2142DX-RAY DIFFRACTIONLocal ncs0.122850.05008
2243DX-RAY DIFFRACTIONLocal ncs0.124270.05008
2244DX-RAY DIFFRACTIONLocal ncs0.124270.05008
2345DX-RAY DIFFRACTIONLocal ncs0.126260.05008
2346DX-RAY DIFFRACTIONLocal ncs0.126260.05008
2447DX-RAY DIFFRACTIONLocal ncs0.117920.05008
2448DX-RAY DIFFRACTIONLocal ncs0.117920.05008
2549DX-RAY DIFFRACTIONLocal ncs0.123840.05008
2550DX-RAY DIFFRACTIONLocal ncs0.123840.05008
2651DX-RAY DIFFRACTIONLocal ncs0.123020.05008
2652DX-RAY DIFFRACTIONLocal ncs0.123020.05008
2753DX-RAY DIFFRACTIONLocal ncs0.124560.05008
2754DX-RAY DIFFRACTIONLocal ncs0.124560.05008
2855DX-RAY DIFFRACTIONLocal ncs0.12260.05008
2856DX-RAY DIFFRACTIONLocal ncs0.12260.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.566-2.6330.2663500.21174650.21380400.9610.97597.20150.216
2.633-2.7050.2972180.22748020.2378050.9580.97364.31770.232
2.705-2.7830.2733770.19369950.19775850.9590.97997.19180.2
2.783-2.8690.2693550.18968500.19373780.9590.9897.65520.196
2.869-2.9630.2423850.18365900.18771470.9610.9897.59340.191
2.963-3.0670.2333250.17762640.1869560.9650.98194.7240.186
3.067-3.1820.2273290.1761430.17366510.9670.98297.30870.181
3.182-3.3120.2173170.17459890.17664140.9710.98298.31620.185
3.312-3.4590.2283090.17557880.17861850.9660.98398.57720.189
3.459-3.6280.2223010.16754380.1758480.9710.98698.13610.18
3.628-3.8240.2112850.16951890.17256020.9730.98497.71510.184
3.824-4.0560.1822770.1549760.15253260.9810.98898.62940.169
4.056-4.3360.1612350.13246320.13449810.9840.9997.71130.153
4.336-4.6830.1492170.11742890.11945970.9870.99298.02040.138
4.683-5.1290.152160.11140160.11342870.9880.99298.7170.131
5.129-5.7330.1662080.13835810.1438410.9850.9998.64620.161
5.733-6.6180.1871700.15531830.15733920.9820.98798.85020.178
6.618-8.1010.1991460.1627350.16228960.9810.98699.4820.189
8.101-11.4350.1971040.16820880.16922010.9780.98499.59110.212
11.435-134.290.29560.25311500.25512220.9460.95298.69070.33

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