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- PDB-5a94: Crystal structure of beta-Glucanase SdGluc5_26A from Saccharophag... -

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Basic information

Entry
Database: PDB / ID: 5a94
TitleCrystal structure of beta-Glucanase SdGluc5_26A from Saccharophagus degradans in complex with tetrasaccharide A, form 1
ComponentsPUTATIVE RETAINING B-GLYCOSIDASE
KeywordsHYDROLASE / CAZYME / GLYCOSIDE HYDROLASE / BETA-GLUCANASE / GH5_26
Function / homology
Function and homology information


glucan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Putative retaining b-glycosidase
Similarity search - Component
Biological speciesSACCHAROPHAGUS DEGRADANS 2-40 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsSulzenbacher, G. / Lafond, M. / Freyd, T. / Henrissat, B. / Coutinho, R.M. / Berrin, J.G. / Garron, M.L.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Quaternary Structure of a Glycoside Hydrolase Dictates Specificity Towards Beta-Glucans
Authors: Lafond, M. / Sulzenbacher, G. / Freyd, T. / Henrissat, B. / Berrin, J.G. / Garron, M.L.
History
DepositionJul 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Structure summary / Category: diffrn_detector / struct / Item: _diffrn_detector.type / _struct.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE RETAINING B-GLYCOSIDASE
B: PUTATIVE RETAINING B-GLYCOSIDASE
C: PUTATIVE RETAINING B-GLYCOSIDASE
D: PUTATIVE RETAINING B-GLYCOSIDASE
E: PUTATIVE RETAINING B-GLYCOSIDASE
F: PUTATIVE RETAINING B-GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,95924
Polymers252,5746
Non-polymers3,38518
Water27,7611541
1
D: PUTATIVE RETAINING B-GLYCOSIDASE
E: PUTATIVE RETAINING B-GLYCOSIDASE
F: PUTATIVE RETAINING B-GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,98012
Polymers126,2873
Non-polymers1,6939
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-91.9 kcal/mol
Surface area37420 Å2
MethodPISA
2
A: PUTATIVE RETAINING B-GLYCOSIDASE
B: PUTATIVE RETAINING B-GLYCOSIDASE
C: PUTATIVE RETAINING B-GLYCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,98012
Polymers126,2873
Non-polymers1,6939
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-93 kcal/mol
Surface area37790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.643, 132.753, 131.352
Angle α, β, γ (deg.)90.00, 133.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-2245-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA30 - 36330 - 363
21LYSLYSBB30 - 36330 - 363
12LYSLYSAA30 - 36430 - 364
22LYSLYSCC30 - 36430 - 364
13ALAALAAA30 - 36230 - 362
23ALAALADD30 - 36230 - 362
14LYSLYSAA30 - 36430 - 364
24LYSLYSEE30 - 36430 - 364
15LYSLYSAA30 - 36430 - 364
25LYSLYSFF30 - 36430 - 364
16LYSLYSBB30 - 36330 - 363
26LYSLYSCC30 - 36330 - 363
17ALAALABB30 - 36230 - 362
27ALAALADD30 - 36230 - 362
18LYSLYSBB30 - 36330 - 363
28LYSLYSEE30 - 36330 - 363
19LYSLYSBB30 - 36330 - 363
29LYSLYSFF30 - 36330 - 363
110ALAALACC30 - 36230 - 362
210ALAALADD30 - 36230 - 362
111LYSLYSCC30 - 36430 - 364
211LYSLYSEE30 - 36430 - 364
112LYSLYSCC30 - 36430 - 364
212LYSLYSFF30 - 36430 - 364
113ALAALADD30 - 36230 - 362
213ALAALAEE30 - 36230 - 362
114ALAALADD30 - 36230 - 362
214ALAALAFF30 - 36230 - 362
115LYSLYSEE30 - 36430 - 364
215LYSLYSFF30 - 36430 - 364

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:
IDCodeMatrixVector
1given(0.4887, 0.7187, 0.4947), (0.6985, 0.01746, -0.7154), (-0.5228, 0.6951, -0.4935)-55.35, 77.58, 37.93
2given(0.4939, 0.6955, -0.5218), (0.7275, -0.001825, 0.6861), (0.4763, -0.7185, -0.5069)-7.007, 13.31, 102.1
3given(-0.5209, 0.6851, 0.5092), (-0.7063, -0.01089, -0.7078), (-0.4794, -0.7284, 0.4896)-7.258, 80.24, 12.35
4given(-0.07382, -0.02131, -0.997), (0.02649, -0.9995, 0.0194), (-0.9969, -0.02498, 0.07435)93.94, 91.07, 0.07226
5given(0.489, -0.7214, 0.4904), (-0.7044, 0.005103, 0.7098), (-0.5145, -0.6925, -0.5056)56.89, 13.56, 57.03

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Components

#1: Protein
PUTATIVE RETAINING B-GLYCOSIDASE / SDGLUC5_26A


Mass: 42095.680 Da / Num. of mol.: 6 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-365 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROPHAGUS DEGRADANS 2-40 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q21KE5, licheninase
#2: Polysaccharide
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1541 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBETA-D-GLUCOPYRANOSYL-(1,3)-BETA-D-GLUCOPYRANOSYL-(1, 4)-BETA-D-GLUCOPYRANOSYL-(1,4)-BETA-D- ...BETA-D-GLUCOPYRANOSYL-(1,3)-BETA-D-GLUCOPYRANOSYL-(1, 4)-BETA-D-GLUCOPYRANOSYL-(1,4)-BETA-D-GLUCOPYRANOSE (CTA): THE REDUCING END GLUCOSE MOIETY IS NOT PRESENT IN THE STRUCTURE

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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: 2.48 Å3/Da / Density % sol: 50.5 % / Description: NONE
Crystal growpH: 7.5
Details: 30% (W/V) PEG 4000, 0.1 M TRIS BUFFER PH 7.5, 0.2 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.95373
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.772
11H+4/2L, -K, -L20.228
ReflectionResolution: 2→47.53 Å / Num. obs: 157114 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 19.67 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WWPDB ENTRY 5A8N

5a8n


Resolution: 1.99→47.42 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.323 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.19038 8001 5.1 %RANDOM
Rwork0.17891 ---
obs0.1795 149108 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.785 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å214.92 Å2
2---5.41 Å20 Å2
3---6.34 Å2
Refinement stepCycle: LAST / Resolution: 1.99→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16604 0 216 1541 18361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0217414
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215936
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9423774
X-RAY DIFFRACTIONr_angle_other_deg1.15336810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65552014
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02224.163836
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.529152771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5111573
X-RAY DIFFRACTIONr_chiral_restr0.0720.22490
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02119360
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024193
X-RAY DIFFRACTIONr_nbd_refined0.2410.25305
X-RAY DIFFRACTIONr_nbd_other0.1830.215148
X-RAY DIFFRACTIONr_nbtor_refined0.1890.28717
X-RAY DIFFRACTIONr_nbtor_other0.0850.28472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2540
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1320.211
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.291
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.23
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1560.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A216590.08
12B216590.08
21A216540.08
22C216540.08
31A217320.07
32D217320.07
41A218420.07
42E218420.07
51A217040.08
52F217040.08
61B215700.08
62C215700.08
71B217000.07
72D217000.07
81B218110.07
82E218110.07
91B217000.08
92F217000.08
101C214950.07
102D214950.07
111C217620.07
112E217620.07
121C216740.08
122F216740.08
131D217110.07
132E217110.07
141D216330.06
142F216330.06
151E218020.08
152F218020.08
LS refinement shellResolution: 1.988→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 446 -
Rwork0.207 8552 -
obs--76.45 %
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)
10.2141-0.18080.00770.25970.10880.20650.00960.0375-0.0092-0.0102-0.0072-0.0088-0.00020.0481-0.00240.0359-0.0018-0.03370.03970.00040.0387-25.51955.4834.675
20.233-0.13780.10860.3131-0.13810.2182-0.0005-0.0208-0.0020.03470.00020.0178-0.0345-0.03340.00030.03840.0048-0.02840.0725-0.00790.0319-10.81635.90772.718
30.05460.01170.11190.38680.06580.4686-0.0132-0.00460.0101-0.04050.0225-0.04490.00460.0605-0.00930.03980.0191-0.02980.0624-0.01130.04190.84718.41932.571
40.78160.2274-0.11260.3153-0.03580.2155-0.00270.13640.0722-0.07140.03830.046-0.0526-0.0733-0.03560.07380.0025-0.04160.08630.04250.057661.64773.0391.188
50.29660.0198-0.06650.3406-0.18350.3276-0.0080.02650.0166-0.03070.01470.04820.009-0.0193-0.00660.0297-0.0002-0.03120.03880.00310.034860.08635.64126.71
60.3422-0.10780.01740.3384-0.21790.28740.018-0.0118-0.0491-0.014-0.01330.0177-0.0063-0.0194-0.00480.04360.0007-0.04590.10790.01050.052821.42556.39814.222
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 364
2X-RAY DIFFRACTION2B30 - 364
3X-RAY DIFFRACTION3C30 - 364
4X-RAY DIFFRACTION4D30 - 364
5X-RAY DIFFRACTION5E30 - 364
6X-RAY DIFFRACTION6F30 - 364

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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

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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

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