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- PDB-2clp: Crystal structure of human aflatoxin B1 aldehyde reductase member 3 -

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Basic information

Entry
Database: PDB / ID: 2clp
TitleCrystal structure of human aflatoxin B1 aldehyde reductase member 3
ComponentsAFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
KeywordsOXIDOREDUCTASE / ALDO-KETO REDUCTASE FAMILY 7 / NAD / NADP / TIM BARREL / SSA REDUCTASE
Function / homology
Function and homology information


aflatoxin catabolic process / cellular aldehyde metabolic process / Aflatoxin activation and detoxification / aldo-keto reductase (NADPH) activity / Oxidoreductases / xenobiotic metabolic process / electron transfer activity / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Aflatoxin B1 aldehyde reductase member 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDebreczeni, J.E. / Marsden, B.D. / Johansson, C. / Kavanagh, K. / Guo, K. / Smee, C. / Gileadi, O. / Turnbull, A. / Papagrigoriou, E. / von Delft, F. ...Debreczeni, J.E. / Marsden, B.D. / Johansson, C. / Kavanagh, K. / Guo, K. / Smee, C. / Gileadi, O. / Turnbull, A. / Papagrigoriou, E. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Sundstrom, M. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Aflatoxin B1 Aldehyde Reductase Member 3
Authors: Debreczeni, J.E. / Johansson, C. / Kavanagh, K. / Turnbull, A. / Papagrigoriou, E. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Sundstrom, M. / Oppermann, U.
History
DepositionApr 28, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 4, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS IN EACH CHAIN ON SHEET RECORDS BELOW IS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
B: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
C: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
D: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
E: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
F: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
G: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
H: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
I: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
J: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
K: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)437,93426
Polymers429,57411
Non-polymers8,36015
Water21612
1
A: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
B: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6355
Polymers78,1042
Non-polymers1,5313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
D: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6355
Polymers78,1042
Non-polymers1,5313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
F: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6355
Polymers78,1042
Non-polymers1,5313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
H: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6355
Polymers78,1042
Non-polymers1,5313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
I: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
J: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5954
Polymers78,1042
Non-polymers1,4912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
K: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
hetero molecules

K: AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5954
Polymers78,1042
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)126.963, 126.963, 490.497
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
12A
22B
32C
42D
52E
62F
72G
82H
92I
102J

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A38 - 95
2111B38 - 95
3111C38 - 95
4111D38 - 95
5111E38 - 95
6111F38 - 95
7111G38 - 95
8111H38 - 95
9111I38 - 95
10111J38 - 95
11111K38 - 95
1211A103 - 360
2211B103 - 360
3211C103 - 360
4211D103 - 360
5211E103 - 360
6211F103 - 360
7211G103 - 360
8211H103 - 360
9211I103 - 360
10211J103 - 360
11211K103 - 360
1121A96 - 102
2121B96 - 102
3121C96 - 102
4121D96 - 102
5121E96 - 102
6121F96 - 102
7121G96 - 102
8121H96 - 102
9121I96 - 102
10121J96 - 102

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.92114, 0.38811, 0.02958), (0.3858, 0.92045, -0.06274), (-0.05158, -0.04638, -0.99759)-0.46333, 0.1532, 0.21906
2given(0.38716, 0.91966, -0.06586), (-0.91324, 0.39233, 0.10987), (0.12688, 0.01761, 0.99176)-101.53127, -47.82928, -14.27185
3given(0.02067, 0.99977, -0.00527), (0.99045, -0.02119, -0.13625), (-0.13633, -0.0024, -0.99066)-117.69337, 32.67796, 85.38853
4given(-0.95205, 0.30376, -0.03637), (-0.30535, -0.95085, 0.05152), (-0.01893, 0.06016, 0.99801)-0.2554, 0.45812, -0.09426
5given(0.99291, -0.11395, 0.03393), (-0.11551, -0.99213, 0.04835), (0.02815, -0.05192, -0.99825)3.23648, 57.26335, 65.88905
6given(0.73909, -0.67254, -0.03792), (0.67258, 0.7399, -0.01351), (0.03714, -0.01552, 0.99919)17.82523, -37.76281, 12.7297
7given(0.73909, -0.67254, -0.03792), (0.67258, 0.7399, -0.01351), (0.03714, -0.01552, 0.99919)17.82523, -37.76281, 12.7297
8given(-0.4811, 0.86624, -0.13476), (-0.87622, -0.48005, 0.04234), (-0.02801, 0.13845, 0.98997)-56.70195, -45.35274, -37.19968
9given(0.78637, 0.61347, 0.07265), (0.6166, -0.78665, -0.03155), (0.03779, 0.0696, -0.99686)-23.92447, 11.14372, 73.95727
10given(-0.25024, -0.9664, 0.0588), (0.96816, -0.24937, 0.0219), (-0.0065, 0.06241, 0.99803)-67.96445, 34.4998, 25.89974

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Components

#1: Protein
AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 3 / AFB1-AR 2


Mass: 39052.223 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 / References: UniProt: O95154
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDISCREPANCIES FOUND IN THE SEQUENCE ARE DUE TO KNOWN DIFFERENCES BETWEEN VARIANTS. THE SEQUENCE ...DISCREPANCIES FOUND IN THE SEQUENCE ARE DUE TO KNOWN DIFFERENCES BETWEEN VARIANTS. THE SEQUENCE USED FOR DESIGNING OUR CONSTRUCT CORRESPONDS TO THE SEQUENCE FOUND IN: GI|19343680 OR BC025709. IN UNIPROT THIS VARIANT IS REFERRED BY THE FTID=VAR_017417

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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: 3 Å3/Da / Density % sol: 58.2 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 600 NL SITTING DROPS 0.05 M CACL2, 10% ETHYLENE-GLYCOL, 0.1 M TRIS PH 8, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.008
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 5, 2005 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3→59.09 Å / Num. obs: 92971 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.98 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.16
Reflection shellResolution: 3→3.1 Å / Redundancy: 4.84 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.22 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BP1
Resolution: 3→164.4 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.892 / SU B: 53.159 / SU ML: 0.423 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.431 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4628 5 %RANDOM
Rwork0.239 ---
obs0.24 88149 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20.89 Å20 Å2
2--1.78 Å20 Å2
3----2.67 Å2
Refinement stepCycle: LAST / Resolution: 3→164.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26897 0 532 12 27441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02128206
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218212
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.96638517
X-RAY DIFFRACTIONr_angle_other_deg1.15344209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52653541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4123.2061176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.506154007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.04515141
X-RAY DIFFRACTIONr_chiral_restr0.0560.24188
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0231827
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025954
X-RAY DIFFRACTIONr_nbd_refined0.2130.26250
X-RAY DIFFRACTIONr_nbd_other0.1830.218304
X-RAY DIFFRACTIONr_nbtor_refined0.1860.213708
X-RAY DIFFRACTIONr_nbtor_other0.0850.213849
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2375
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.237
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3271.518239
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.547227891
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.808311818
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3474.510626
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3917tight positional0.030.05
12B3917tight positional0.020.05
13C3917tight positional0.020.05
14D3917tight positional0.020.05
15E3917tight positional0.020.05
16F3917tight positional0.050.05
17G3917tight positional0.020.05
18H3917tight positional0.040.05
19I3917tight positional0.020.05
110J3917tight positional0.020.05
111K3917tight positional0.030.05
21A55tight positional0.020.05
22B55tight positional0.020.05
23C55tight positional0.020.05
24D55tight positional0.020.05
25E55tight positional0.020.05
26F55tight positional0.020.05
27G55tight positional0.020.05
28H55tight positional0.020.05
29I55tight positional0.020.05
210J55tight positional0.020.05
11A3917tight thermal2.1799
12B3917tight thermal1.9299
13C3917tight thermal2.4499
14D3917tight thermal2.4199
15E3917tight thermal2.2499
16F3917tight thermal2.2999
17G3917tight thermal2.3899
18H3917tight thermal2.2499
19I3917tight thermal2.0999
110J3917tight thermal2.0699
111K3917tight thermal2.3299
21A55tight thermal2.8999
22B55tight thermal1.9799
23C55tight thermal1.1599
24D55tight thermal0.5699
25E55tight thermal3.8499
26F55tight thermal2.8399
27G55tight thermal1.3599
28H55tight thermal3.2899
29I55tight thermal1.0999
210J55tight thermal0.7399
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.403 320
Rwork0.393 6337
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.40980.49610.15862.79480.56255.7681-0.40650.1865-0.19120.06980.0278-0.1690.84240.9820.3787-0.25670.18950.1623-0.42280.0927-0.3698-10.976325.342657.9276
22.07480.00120.46783.7949-0.90054.978-0.0962-0.09210.06360.3535-0.23930.43140.2123-1.55820.3355-0.3814-0.1230.22210.0083-0.2253-0.2916-46.895332.306949.087
33.80620.27780.89311.6831-0.3015.10920.0970.3532-0.3435-0.02510.0233-0.12911.14090.2367-0.1204-0.41190.1334-0.0794-0.0461-0.1822-0.3702-86.2911-21.499642.2693
43.33090.2876-0.59191.5325-0.77274.7581-0.0809-0.29710.24520.16730.0695-0.053-1.2201-0.07390.0115-0.38120.0896-0.0281-0.045-0.1668-0.3721-93.111713.271729.3346
52.38810.0495-0.24244.444-0.48843.4351-0.05860.0660.0504-0.5354-0.14860.38180.1415-0.99750.2072-0.3907-0.0248-0.0225-0.0687-0.1955-0.3183-45.404332.711213.2515
62.3141-0.7183-0.57473.34470.55014.30150.028-0.11760.1551-0.0422-0.1437-0.2177-0.12850.60380.1156-0.36620.11130.0692-0.42640.0218-0.3656-8.574536.23336.4823
72.9842-0.8769-0.88713.00940.63425.2664-0.28130.37060.0329-0.11490.02870.0377-0.31840.72160.2527-0.1887-0.4771-0.0958-0.31580.1664-0.3628-9.5358-27.28569.8438
83.2072-1.0355-0.10333.7204-0.16213.2741-0.35470.5095-0.38050.0046-0.09890.58370.5848-1.08650.4537-0.0884-0.61630.06620.1804-0.2266-0.0003-40.166-46.126859.7311
93.5523-1.4197-0.55233.20260.01683.3633-0.0330.8239-0.5677-0.3885-0.29970.48040.6658-0.98980.33260.3432-0.7189-0.08650.7028-0.49310.0545-37.2228-45.398824.008
103.773-1.058-0.83242.9327-0.37212.54640.3083-0.16690.5256-0.2603-0.1533-0.2527-0.23970.1379-0.1550.3891-0.51350.12110.3949-0.31970.1169-12.8006-17.379617.5214
113.75240.1636-0.61062.00180.51625.25740.212-0.05680.2335-0.23910.0705-0.2236-1.00590.3437-0.2825-0.3746-0.05180.1817-0.36540.0104-0.4279-86.295618.912385.3833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 360
2X-RAY DIFFRACTION2B38 - 360
3X-RAY DIFFRACTION3C38 - 360
4X-RAY DIFFRACTION4D38 - 360
5X-RAY DIFFRACTION5E38 - 360
6X-RAY DIFFRACTION6F38 - 360
7X-RAY DIFFRACTION7G38 - 360
8X-RAY DIFFRACTION8H38 - 360
9X-RAY DIFFRACTION9I38 - 360
10X-RAY DIFFRACTION10J38 - 360
11X-RAY DIFFRACTION11K38 - 360

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Major update of PDB

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  • 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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