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- PDB-7x32: Crystal structure of E. coli NfsB in complex with berberine -

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Basic information

Entry
Database: PDB / ID: 7x32
TitleCrystal structure of E. coli NfsB in complex with berberine
ComponentsDihydropteridine reductase
KeywordsOXIDOREDUCTASE / nitroreductase / berberine
Function / homology
Function and homology information


oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / 6,7-dihydropteridine reductase / 2,4,6-trinitrotoluene catabolic process / 6,7-dihydropteridine reductase activity / Oxidoreductases / nucleotide binding / cytosol
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / : / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
BERBERINE / FLAVIN MONONUCLEOTIDE / Dihydropteridine reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.829 Å
AuthorsZhang, H. / Wen, H.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970152 China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural basis for the transformation of the traditional medicine berberine by bacterial nitroreductase.
Authors: Wen, H.Y. / Pan, L.B. / Ma, S.R. / Yang, X.Y. / Hu, J.C. / Zhao, H.F. / Gao, Z.Q. / Dong, Y.H. / Wang, Y. / Zhang, H.
History
DepositionFeb 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydropteridine reductase
B: Dihydropteridine reductase
C: Dihydropteridine reductase
D: Dihydropteridine reductase
E: Dihydropteridine reductase
F: Dihydropteridine reductase
G: Dihydropteridine reductase
H: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,57530
Polymers191,4978
Non-polymers6,07822
Water17,475970
1
A: Dihydropteridine reductase
C: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2947
Polymers47,8742
Non-polymers1,4195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-38 kcal/mol
Surface area16860 Å2
MethodPISA
2
B: Dihydropteridine reductase
H: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3728
Polymers47,8742
Non-polymers1,4976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10350 Å2
ΔGint-36 kcal/mol
Surface area16730 Å2
MethodPISA
3
D: Dihydropteridine reductase
F: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2947
Polymers47,8742
Non-polymers1,4195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint-45 kcal/mol
Surface area16750 Å2
MethodPISA
4
E: Dihydropteridine reductase
G: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6168
Polymers47,8742
Non-polymers1,7426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-31 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.466, 77.941, 116.128
Angle α, β, γ (deg.)74.050, 79.440, 74.260
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 3:24 or resseq 26:54 or resseq...
21(chain B and (resseq 3:24 or resseq 26:54 or resseq...
31(chain C and (resseq 3:24 or resseq 26:54 or resseq...
41(chain D and (resseq 3:24 or resseq 26:54 or resseq...
51(chain E and (resseq 3:24 or resseq 26:54 or resseq...
61(chain F and (resseq 3:24 or resseq 26:54 or resseq...
71(chain G and (resseq 3:24 or resseq 26:54 or resseq...
81(chain H and (resseq 3:24 or resseq 26:54 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 3:24 or resseq 26:54 or resseq...A3 - 24
121(chain A and (resseq 3:24 or resseq 26:54 or resseq...A26 - 54
131(chain A and (resseq 3:24 or resseq 26:54 or resseq...A1
141(chain A and (resseq 3:24 or resseq 26:54 or resseq...A113 - 118
151(chain A and (resseq 3:24 or resseq 26:54 or resseq...A2 - 217
161(chain A and (resseq 3:24 or resseq 26:54 or resseq...A120 - 123
171(chain A and (resseq 3:24 or resseq 26:54 or resseq...A2 - 217
181(chain A and (resseq 3:24 or resseq 26:54 or resseq...A2 - 217
191(chain A and (resseq 3:24 or resseq 26:54 or resseq...A2 - 217
1101(chain A and (resseq 3:24 or resseq 26:54 or resseq...A2 - 217
1111(chain A and (resseq 3:24 or resseq 26:54 or resseq...A2 - 217
1121(chain A and (resseq 3:24 or resseq 26:54 or resseq...A2 - 217
1131(chain A and (resseq 3:24 or resseq 26:54 or resseq...A2 - 217
211(chain B and (resseq 3:24 or resseq 26:54 or resseq...B3 - 24
221(chain B and (resseq 3:24 or resseq 26:54 or resseq...B26 - 54
231(chain B and (resseq 3:24 or resseq 26:54 or resseq...B56 - 72
241(chain B and (resseq 3:24 or resseq 26:54 or resseq...B74 - 111
251(chain B and (resseq 3:24 or resseq 26:54 or resseq...B120 - 123
261(chain B and (resseq 3:24 or resseq 26:54 or resseq...B2 - 217
271(chain B and (resseq 3:24 or resseq 26:54 or resseq...B2 - 217
281(chain B and (resseq 3:24 or resseq 26:54 or resseq...B2 - 217
291(chain B and (resseq 3:24 or resseq 26:54 or resseq...B2 - 217
2101(chain B and (resseq 3:24 or resseq 26:54 or resseq...B2 - 217
2111(chain B and (resseq 3:24 or resseq 26:54 or resseq...B2 - 217
2121(chain B and (resseq 3:24 or resseq 26:54 or resseq...B2 - 217
2131(chain B and (resseq 3:24 or resseq 26:54 or resseq...B2 - 217
311(chain C and (resseq 3:24 or resseq 26:54 or resseq...C3 - 24
321(chain C and (resseq 3:24 or resseq 26:54 or resseq...C26 - 54
331(chain C and (resseq 3:24 or resseq 26:54 or resseq...C56 - 72
341(chain C and (resseq 3:24 or resseq 26:54 or resseq...C74 - 111
351(chain C and (resseq 3:24 or resseq 26:54 or resseq...C113 - 118
361(chain C and (resseq 3:24 or resseq 26:54 or resseq...C120 - 123
371(chain C and (resseq 3:24 or resseq 26:54 or resseq...C124
381(chain C and (resseq 3:24 or resseq 26:54 or resseq...C2 - 217
391(chain C and (resseq 3:24 or resseq 26:54 or resseq...C2 - 217
3101(chain C and (resseq 3:24 or resseq 26:54 or resseq...C2 - 217
3111(chain C and (resseq 3:24 or resseq 26:54 or resseq...C2 - 217
3121(chain C and (resseq 3:24 or resseq 26:54 or resseq...C2 - 217
3131(chain C and (resseq 3:24 or resseq 26:54 or resseq...C2 - 217
3141(chain C and (resseq 3:24 or resseq 26:54 or resseq...C2 - 217
411(chain D and (resseq 3:24 or resseq 26:54 or resseq...D3 - 24
421(chain D and (resseq 3:24 or resseq 26:54 or resseq...D26 - 54
431(chain D and (resseq 3:24 or resseq 26:54 or resseq...D56 - 72
441(chain D and (resseq 3:24 or resseq 26:54 or resseq...D120 - 123
451(chain D and (resseq 3:24 or resseq 26:54 or resseq...D2 - 217
461(chain D and (resseq 3:24 or resseq 26:54 or resseq...D120 - 123
471(chain D and (resseq 3:24 or resseq 26:54 or resseq...D2 - 217
481(chain D and (resseq 3:24 or resseq 26:54 or resseq...D2 - 217
491(chain D and (resseq 3:24 or resseq 26:54 or resseq...D2 - 217
4101(chain D and (resseq 3:24 or resseq 26:54 or resseq...D2 - 217
4111(chain D and (resseq 3:24 or resseq 26:54 or resseq...D2 - 217
4121(chain D and (resseq 3:24 or resseq 26:54 or resseq...D2 - 217
511(chain E and (resseq 3:24 or resseq 26:54 or resseq...E3 - 24
521(chain E and (resseq 3:24 or resseq 26:54 or resseq...E26 - 54
531(chain E and (resseq 3:24 or resseq 26:54 or resseq...E1
541(chain E and (resseq 3:24 or resseq 26:54 or resseq...E8
551(chain E and (resseq 3:24 or resseq 26:54 or resseq...E120 - 123
561(chain E and (resseq 3:24 or resseq 26:54 or resseq...E1 - 217
571(chain E and (resseq 3:24 or resseq 26:54 or resseq...E1 - 217
581(chain E and (resseq 3:24 or resseq 26:54 or resseq...E1 - 217
591(chain E and (resseq 3:24 or resseq 26:54 or resseq...E1 - 217
5101(chain E and (resseq 3:24 or resseq 26:54 or resseq...E1 - 217
5111(chain E and (resseq 3:24 or resseq 26:54 or resseq...E1 - 217
5121(chain E and (resseq 3:24 or resseq 26:54 or resseq...E1 - 217
5131(chain E and (resseq 3:24 or resseq 26:54 or resseq...E1 - 217
5141(chain E and (resseq 3:24 or resseq 26:54 or resseq...E1 - 217
611(chain F and (resseq 3:24 or resseq 26:54 or resseq...F3 - 24
621(chain F and (resseq 3:24 or resseq 26:54 or resseq...F26 - 54
631(chain F and (resseq 3:24 or resseq 26:54 or resseq...F56 - 72
641(chain F and (resseq 3:24 or resseq 26:54 or resseq...F74 - 111
651(chain F and (resseq 3:24 or resseq 26:54 or resseq...F120 - 123
661(chain F and (resseq 3:24 or resseq 26:54 or resseq...F2 - 217
671(chain F and (resseq 3:24 or resseq 26:54 or resseq...F2 - 217
681(chain F and (resseq 3:24 or resseq 26:54 or resseq...F2 - 217
691(chain F and (resseq 3:24 or resseq 26:54 or resseq...F2 - 217
6101(chain F and (resseq 3:24 or resseq 26:54 or resseq...F2 - 217
6111(chain F and (resseq 3:24 or resseq 26:54 or resseq...F2 - 217
6121(chain F and (resseq 3:24 or resseq 26:54 or resseq...F2 - 217
6131(chain F and (resseq 3:24 or resseq 26:54 or resseq...F2 - 217
711(chain G and (resseq 3:24 or resseq 26:54 or resseq...G3 - 24
721(chain G and (resseq 3:24 or resseq 26:54 or resseq...G26 - 54
731(chain G and (resseq 3:24 or resseq 26:54 or resseq...G1
741(chain G and (resseq 3:24 or resseq 26:54 or resseq...G113 - 118
751(chain G and (resseq 3:24 or resseq 26:54 or resseq...G120
761(chain G and (resseq 3:24 or resseq 26:54 or resseq...G1 - 217
771(chain G and (resseq 3:24 or resseq 26:54 or resseq...G1 - 217
781(chain G and (resseq 3:24 or resseq 26:54 or resseq...G1 - 217
791(chain G and (resseq 3:24 or resseq 26:54 or resseq...G1 - 217
7101(chain G and (resseq 3:24 or resseq 26:54 or resseq...G1 - 217
7111(chain G and (resseq 3:24 or resseq 26:54 or resseq...G1 - 217
7121(chain G and (resseq 3:24 or resseq 26:54 or resseq...G1 - 217
7131(chain G and (resseq 3:24 or resseq 26:54 or resseq...G1 - 217
7141(chain G and (resseq 3:24 or resseq 26:54 or resseq...G1 - 217
811(chain H and (resseq 3:24 or resseq 26:54 or resseq...H3 - 24
821(chain H and (resseq 3:24 or resseq 26:54 or resseq...H26 - 54
831(chain H and (resseq 3:24 or resseq 26:54 or resseq...H1
841(chain H and (resseq 3:24 or resseq 26:54 or resseq...H113 - 118
851(chain H and (resseq 3:24 or resseq 26:54 or resseq...H120
861(chain H and (resseq 3:24 or resseq 26:54 or resseq...H2 - 217
871(chain H and (resseq 3:24 or resseq 26:54 or resseq...H2 - 217
881(chain H and (resseq 3:24 or resseq 26:54 or resseq...H2 - 217
891(chain H and (resseq 3:24 or resseq 26:54 or resseq...H2 - 217
8101(chain H and (resseq 3:24 or resseq 26:54 or resseq...H2 - 217
8111(chain H and (resseq 3:24 or resseq 26:54 or resseq...H2 - 217
8121(chain H and (resseq 3:24 or resseq 26:54 or resseq...H2 - 217
8131(chain H and (resseq 3:24 or resseq 26:54 or resseq...H2 - 217
8141(chain H and (resseq 3:24 or resseq 26:54 or resseq...H2 - 217

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Dihydropteridine reductase / Dihydropteridine reductase / NAD(P)H-dependent / oxygen-insensitive / NAD(P)H nitroreductase / ...Dihydropteridine reductase / NAD(P)H-dependent / oxygen-insensitive / NAD(P)H nitroreductase / NAD(P)H-dependent oxidoreductase / Oxygen-insensitive NAD(P)H nitroreductase


Mass: 23937.182 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: nfnB, nfsB, A8W81_002651, ACU57_25670, AUQ29_26440, BANRA_01861, BANRA_03752, BJI68_06040, BO068_003897, BON73_00805, BUE81_05150, BvCms2454_01694, C5F72_18880, C5N07_20565, CA593_00340, D0X26_ ...Gene: nfnB, nfsB, A8W81_002651, ACU57_25670, AUQ29_26440, BANRA_01861, BANRA_03752, BJI68_06040, BO068_003897, BON73_00805, BUE81_05150, BvCms2454_01694, C5F72_18880, C5N07_20565, CA593_00340, D0X26_22115, DM968_16990, E2119_24050, E4K51_19485, E4K54_19475, EC3234A_5c00510, EI041_22215, EL79_3302, EL80_3257, F2N31_21430, F9V24_20200, FV293_23750, GF646_21790, GKF86_15175, GKF89_11335, GRW05_08435, GRW81_04890, H4P50_18485, H4P51_18335, HNC52_17915, HX136_18760, NCTC8008_03225, NCTC9045_04181, NCTC9048_02746, SAMEA3753300_04152, WP2S18E08_33810
Production host: Escherichia coli (E. coli)
References: UniProt: A0A094VLP5, 6,7-dihydropteridine reductase, Oxidoreductases

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Non-polymers , 5 types, 992 molecules

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-BER / BERBERINE


Mass: 336.361 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H18NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 970 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.41 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2% v/v Tacsimate, 0.1 M Sodium acetate trihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.829→55 Å / Num. obs: 151398 / % possible obs: 92.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.05 / Rrim(I) all: 0.071 / Net I/σ(I): 12.2
Reflection shellResolution: 1.829→1.93 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 22921 / CC1/2: 0.878 / Rpim(I) all: 0.353 / Rrim(I) all: 0.499 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ICU

1icu


Resolution: 1.829→54.928 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 7589 5.01 %
Rwork0.2046 143788 -
obs0.2064 151377 92.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.76 Å2 / Biso mean: 32.0668 Å2 / Biso min: 13.64 Å2
Refinement stepCycle: final / Resolution: 1.829→54.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13431 0 415 970 14816
Biso mean--33.09 35.8 -
Num. residues----1730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01514182
X-RAY DIFFRACTIONf_angle_d1.59319269
X-RAY DIFFRACTIONf_chiral_restr0.0922121
X-RAY DIFFRACTIONf_plane_restr0.0092430
X-RAY DIFFRACTIONf_dihedral_angle_d12.148347
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7583X-RAY DIFFRACTION9.636TORSIONAL
12B7583X-RAY DIFFRACTION9.636TORSIONAL
13C7583X-RAY DIFFRACTION9.636TORSIONAL
14D7583X-RAY DIFFRACTION9.636TORSIONAL
15E7583X-RAY DIFFRACTION9.636TORSIONAL
16F7583X-RAY DIFFRACTION9.636TORSIONAL
17G7583X-RAY DIFFRACTION9.636TORSIONAL
18H7583X-RAY DIFFRACTION9.636TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8293-1.85010.31382650.2572504996
1.8501-1.87190.29522680.2492486896
1.8719-1.89470.2982640.248499496
1.8947-1.91870.28862660.2466494196
1.9187-1.94390.29942540.2413500696
1.9439-1.97050.26892750.2305492096
1.9705-1.99870.2772710.2387494696
1.9987-2.02850.30692420.2338494796
2.0285-2.06020.29932290.2451401591
2.0602-2.0940.2433810.2331136693
2.094-2.13010.2772760.2284501796
2.1301-2.16890.28642690.2258495796
2.1689-2.21060.28442880.2203498796
2.2106-2.25570.24152460.2226501097
2.2557-2.30470.27692800.2166500597
2.3047-2.35840.2732680.2191498197
2.3584-2.41730.27472430.2219499796
2.4173-2.48270.27642460.226503897
2.4827-2.55580.27942510.217497197
2.5558-2.63820.24682500.2108504497
2.6382-2.73250.26282770.2125505397
2.7325-2.84190.26132510.2159501297
2.8419-2.97130.25212540.2132503197
2.9713-3.12790.2572400.2009499896
3.1279-3.32390.21452910.2031499597
3.3239-3.58040.23142640.1969500397
3.5804-3.94070.19022000.1912355669
3.9407-4.51070.19872530.1672502797
4.5107-5.6820.19712760.1763502697
5.682-54.90.21172510.1872502897

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