[English] 日本語
Yorodumi
- PDB-2bfg: crystal structure of beta-xylosidase (fam GH39) in complex with d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bfg
Titlecrystal structure of beta-xylosidase (fam GH39) in complex with dinitrophenyl-beta-xyloside and covalently bound xyloside
ComponentsBETA-XYLOSIDASEXylan 1,4-b-xylosidase
KeywordsHYDROLASE / FAMILY GH39 / THERMOPHILIC ENZYME
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / xylan catabolic process
Similarity search - Function
Glycosyl hydrolase domain; family 39 / : / : / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Glycosyl hydrolase domain; family 39 / : / : / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2,5-DINITROPHENOL / beta-D-xylopyranose / alpha-D-xylopyranose / Beta-xylosidase
Similarity search - Component
Biological speciesBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCzjzek, M. / Bravman, T. / Henrissat, B. / Shoham, Y.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Enzyme-Substrate Complex Structures of a Gh39 Beta-Xylosidase from Geobacillus Stearothermophilus.
Authors: Czjzek, M. / David, A.B. / Bravman, T. / Shoham, G. / Henrissat, B. / Shoham, Y.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and Preliminary X-Ray Analysis of Family 39 Beta-D-Xylosidase from Geobacillus Stearothermophilus T-6
Authors: Czjzek, M. / Bravman, T. / Henrissat, B. / Shoham, Y.
History
DepositionDec 7, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 14, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.ndb_seq_num / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB, BC, CB" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB, BC, CB" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 8-STRANDED BARRELS REPRESENTED BY 9-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DB, EC, FB, GB, HB" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 7-STRANDED BARRELS THIS IS REPRESENTED BY 8-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-XYLOSIDASE
B: BETA-XYLOSIDASE
C: BETA-XYLOSIDASE
D: BETA-XYLOSIDASE
E: BETA-XYLOSIDASE
F: BETA-XYLOSIDASE
G: BETA-XYLOSIDASE
H: BETA-XYLOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,82836
Polymers464,0068
Non-polymers2,82228
Water24,8611380
1
A: BETA-XYLOSIDASE
B: BETA-XYLOSIDASE
C: BETA-XYLOSIDASE
D: BETA-XYLOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,74820
Polymers232,0034
Non-polymers1,74516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21070 Å2
ΔGint-169.5 kcal/mol
Surface area65720 Å2
MethodPISA
2
E: BETA-XYLOSIDASE
F: BETA-XYLOSIDASE
G: BETA-XYLOSIDASE
H: BETA-XYLOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,08016
Polymers232,0034
Non-polymers1,07712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19780 Å2
ΔGint-150.2 kcal/mol
Surface area66010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.950, 162.160, 308.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYARGARG5AA2 - 652 - 65
21GLYGLYARGARG5BB2 - 652 - 65
31GLYGLYARGARG5CC2 - 652 - 65
41GLYGLYARGARG5DD2 - 652 - 65
51GLYGLYARGARG5EE2 - 652 - 65
61GLYGLYARGARG5FF2 - 652 - 65
71GLYGLYARGARG5GG2 - 652 - 65
81GLYGLYARGARG5HH2 - 652 - 65
12GLUGLUPROPRO6AA66 - 7566 - 75
22GLUGLUPROPRO6BB66 - 7566 - 75
32GLUGLUPROPRO6CC66 - 7566 - 75
42GLUGLUPROPRO6DD66 - 7566 - 75
52GLUGLUPROPRO6EE66 - 7566 - 75
62GLUGLUPROPRO6FF66 - 7566 - 75
72GLUGLUPROPRO6GG66 - 7566 - 75
82GLUGLUPROPRO6HH66 - 7566 - 75
13PHEPHELEULEU5AA76 - 40076 - 400
23PHEPHELEULEU5BB76 - 40076 - 400
33PHEPHELEULEU5CC76 - 40076 - 400
43PHEPHELEULEU5DD76 - 40076 - 400
53PHEPHELEULEU5EE76 - 40076 - 400
63PHEPHELEULEU5FF76 - 40076 - 400
73PHEPHELEULEU5GG76 - 40076 - 400
83PHEPHELEULEU5HH76 - 40076 - 400
14VALVALPHEPHE6AA401 - 410401 - 410
24VALVALPHEPHE6BB401 - 410401 - 410
34VALVALPHEPHE6CC401 - 410401 - 410
44VALVALPHEPHE6DD401 - 410401 - 410
54VALVALPHEPHE6EE401 - 410401 - 410
64VALVALPHEPHE6FF401 - 410401 - 410
74VALVALPHEPHE6GG401 - 410401 - 410
84VALVALPHEPHE6HH401 - 410401 - 410
15ILEILEGLUGLU5AA411 - 455411 - 455
25ILEILEGLUGLU5BB411 - 455411 - 455
35ILEILEGLUGLU5CC411 - 455411 - 455
45ILEILEGLUGLU5DD411 - 455411 - 455
55ILEILEGLUGLU5EE411 - 455411 - 455
65ILEILEGLUGLU5FF411 - 455411 - 455
75ILEILEGLUGLU5GG411 - 455411 - 455
85ILEILEGLUGLU5HH411 - 455411 - 455
16GLNGLNHISHIS6AA456 - 465456 - 465
26GLNGLNHISHIS6BB456 - 465456 - 465
36GLNGLNHISHIS6CC456 - 465456 - 465
46GLNGLNHISHIS6DD456 - 465456 - 465
56GLNGLNHISHIS6EE456 - 465456 - 465
66GLNGLNHISHIS6FF456 - 465456 - 465
76GLNGLNHISHIS6GG456 - 465456 - 465
86GLNGLNHISHIS6HH456 - 465456 - 465
17LEULEUSERSER5AA466 - 502466 - 502
27LEULEUSERSER5BB466 - 502466 - 502
37LEULEUSERSER5CC466 - 502466 - 502
47LEULEUSERSER5DD466 - 502466 - 502
57LEULEUSERSER5EE466 - 502466 - 502
67LEULEUSERSER5FF466 - 502466 - 502
77LEULEUSERSER5GG466 - 502466 - 502
87LEULEUSERSER5HH466 - 502466 - 502

NCS oper:
IDCodeMatrixVector
1given(-0.99968, -0.00126, 0.02513), (0.00154, -0.99994, 0.01118), (0.02511, 0.01121, 0.99962)42.93671, 133.20541, -1.18912
2given(0.97575, 0.21847, -0.01354), (0.21844, -0.97584, -0.00404), (-0.0141, 0.00099, -0.9999)-13.36314, 127.79912, 133.86832
3given(-0.97608, -0.21729, -0.00716), (-0.21722, 0.97607, -0.01021), (0.00921, -0.00841, -0.99992)59.13493, 7.10354, 133.90971
4given(-0.98729, 0.0868, 0.13317), (-0.08454, -0.99616, 0.02255), (0.13461, 0.01101, 0.99084)27.46934, 148.10074, 74.57674
5given(0.9905, -0.08696, 0.10648), (0.08628, 0.99621, 0.01098), (-0.10703, -0.00169, 0.99425)-3.21161, 11.55622, 80.72701
6given(-0.94605, -0.30517, -0.10893), (-0.30567, 0.95206, -0.01254), (0.10753, 0.02144, -0.99397)68.9648, 24.82551, 206.85515
7given(0.94412, 0.30119, -0.13385), (0.30146, -0.95329, -0.01879), (-0.13326, -0.02261, -0.99082)-12.39018, 139.35812, 215.03404

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
BETA-XYLOSIDASE / Xylan 1,4-b-xylosidase / 1 / 4-BETA-D-XYLAN XYLOHYDROLASE / XYLAN 1 / 4-BETA-XYLOSIDASE


Mass: 58000.793 Da / Num. of mol.: 8 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COVALENT GLYCOSYL-ENZYME INTERMEDIATE LINKS BETWEEN A 278 AND A 512 B 278 AND B 505 C 278 AND C 506 D 278 AND D 513 E 278 AND E 508 F 278 AND F 509 G 278 AND G 510 H 278 AND H 511
Source: (gene. exp.) BACILLUS STEAROTHERMOPHILUS (bacteria) / Strain: T-6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9ZFM2, xylan 1,4-beta-xylosidase

-
Sugars , 2 types, 10 molecules

#4: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose / Xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar
ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE / Xylose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 1398 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ANX / 2,5-DINITROPHENOL / Dinitrophenol


Mass: 184.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4N2O5
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1380 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUES CHAINS A-H, GLU 160 ALA
Sequence detailsTHE SEQUENCE OF THE UNIPROT DATABASE CONTAINS TWO STRETCHES OF ERRORS THAT HAVE BEEN REVEALED BY ...THE SEQUENCE OF THE UNIPROT DATABASE CONTAINS TWO STRETCHES OF ERRORS THAT HAVE BEEN REVEALED BY THE CRYSTAL STRUCTURE AND CONFIRMED BY THE AUTHORS OF THE UNIPROT ENTRY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growpH: 7.5
Details: PEG 8000 20 % (W/V), 50 MM NACL, 100 MM HEPES PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 10, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 186001 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.1
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UHV

1uhv


Resolution: 2.4→40.11 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.871 / SU B: 6.049 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.523 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 8689 5 %RANDOM
Rwork0.194 ---
obs0.198 165095 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.89 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å20 Å20 Å2
2---2.37 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32693 0 164 1380 34237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.02233822
X-RAY DIFFRACTIONr_bond_other_d0.0020.0230077
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.93845846
X-RAY DIFFRACTIONr_angle_other_deg0.892369843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46754000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.24894
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0237452
X-RAY DIFFRACTIONr_gen_planes_other0.0060.027376
X-RAY DIFFRACTIONr_nbd_refined0.2130.210037
X-RAY DIFFRACTIONr_nbd_other0.2490.243358
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.220843
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.22174
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.2124
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2970.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5481.519968
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.045232415
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.702313854
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8484.513431
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2771medium positional0.20.5
2B2771medium positional0.170.5
3C2771medium positional0.180.5
4D2771medium positional0.180.5
5E2771medium positional0.20.5
6F2771medium positional0.190.5
7G2771medium positional0.160.5
8H2771medium positional0.230.5
1A5055loose positional0.515
2B5055loose positional0.55
3C5055loose positional0.55
4D5055loose positional0.535
5E5055loose positional0.515
6F5055loose positional0.525
7G5055loose positional0.435
8H5055loose positional0.555
1A2771medium thermal0.492
2B2771medium thermal0.472
3C2771medium thermal0.52
4D2771medium thermal0.522
5E2771medium thermal0.552
6F2771medium thermal0.622
7G2771medium thermal0.562
8H2771medium thermal0.562
1A5055loose thermal1.5210
2B5055loose thermal1.610
3C5055loose thermal1.3810
4D5055loose thermal1.510
5E5055loose thermal1.7910
6F5055loose thermal1.710
7G5055loose thermal1.610
8H5055loose thermal1.610
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.397 610
Rwork0.328 12066
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.15590.11540.0070.4688-0.2190.3122-0.00110.0114-0.0215-0.0290.01280.0564-0.0518-0.0225-0.01170.0040.0194-0.00180.1103-0.00140.0795.73382.90251.385
20.21140.12830.0860.57670.15680.23230.0040.0521-0.0046-0.1034-0.0018-0.08410.03220.0673-0.00210.00460.0231-0.0090.14870.00330.085338.41450.98151.241
30.2212-0.15390.07230.4118-0.11760.2575-0.0106-0.0443-0.0380.10490.03520.08860.0192-0.0364-0.02470.0338-0.00450.02340.12050.01770.09479.71547.87182.421
40.1201-0.1096-0.00860.48140.1420.2012-0.0294-0.0001-0.00840.17550.0044-0.0795-0.0410.04050.0250.0888-0.0221-0.04750.12150.00750.081235.0186.29781.902
50.11460.1035-0.01480.29390.14990.2746-0.0040.0060.0071-0.0750.0178-0.002-0.02130.0298-0.01380.06640.00430.01620.1044-0.0060.063835.82766.202127.171
60.21270.16520.00110.4098-0.01890.1702-0.0570.03240.0285-0.17030.030.0709-0.0858-0.03970.0270.13510.0103-0.05090.1234-0.00830.09960.7795.206131.061
70.0901-0.1258-0.08580.28140.19110.2325-0.0153-0.0128-0.0131-0.06080.0306-0.0176-0.04860.0368-0.01530.0595-0.01830.01380.0958-0.01220.063432.607101.384158.143
80.2514-0.110.1540.2424-0.04910.1804-0.0146-0.0229-0.00080.03660.0030.04520.0149-0.04040.01160.0435-0.00360.02450.1053-0.00160.076511.18761.084161.45
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 502
2X-RAY DIFFRACTION2B2 - 502
3X-RAY DIFFRACTION3C2 - 502
4X-RAY DIFFRACTION4D2 - 502
5X-RAY DIFFRACTION5E2 - 502
6X-RAY DIFFRACTION6F2 - 502
7X-RAY DIFFRACTION7G2 - 502
8X-RAY DIFFRACTION8H2 - 502

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more