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- PDB-7ypv: Crystal structure of OrE-ST-F -

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Basic information

Entry
Database: PDB / ID: 7ypv
TitleCrystal structure of OrE-ST-F
ComponentsAcetyltransferase
KeywordsTRANSFERASE / acetyltransferase streptothricin F
Function / homologypeptide-alanine-alpha-N-acetyltransferase activity / : / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Streptothricin F / Acetyltransferase
Function and homology information
Biological speciesStreptomyces lavendulae subsp. lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.415 Å
AuthorsWang, Y.L. / Li, T.L.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry.
Authors: Wang, Y.L. / Chang, C.Y. / Hsu, N.S. / Lo, I.W. / Lin, K.H. / Chen, C.L. / Chang, C.F. / Wang, Z.C. / Ogasawara, Y. / Dairi, T. / Maruyama, C. / Hamano, Y. / Li, T.L.
History
DepositionAug 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)180,59216
Polymers176,5728
Non-polymers4,0208
Water9,674537
1
A: Acetyltransferase
B: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1484
Polymers44,1432
Non-polymers1,0052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-11 kcal/mol
Surface area16800 Å2
MethodPISA
2
C: Acetyltransferase
D: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1484
Polymers44,1432
Non-polymers1,0052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-11 kcal/mol
Surface area16650 Å2
MethodPISA
3
E: Acetyltransferase
F: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1484
Polymers44,1432
Non-polymers1,0052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-11 kcal/mol
Surface area16580 Å2
MethodPISA
4
G: Acetyltransferase
H: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1484
Polymers44,1432
Non-polymers1,0052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-11 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.714, 77.826, 108.990
Angle α, β, γ (deg.)89.945, 90.043, 89.991
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74A
84E
95A
105F
116A
126G
137A
147H
158B
168C
179B
189D
1910B
2010E
2111B
2211F
2312B
2412G
2513B
2613H
2714C
2814D
2915C
3015E
3116C
3216F
3317C
3417G
3518C
3618H
3719D
3819E
3920D
4020F
4121D
4221G
4322D
4422H
4523E
4623F
4724E
4824G
4925E
5025H
5126F
5226G
5327F
5427H
5528G
5628H

NCS domain segments:

Beg auth comp-ID: THR / Beg label comp-ID: THR

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROAA8 - 18428 - 204
221PROPROBB8 - 18428 - 204
332PROPROAA8 - 18428 - 204
442PROPROCC8 - 18428 - 204
553CYSCYSAA7 - 18527 - 205
663CYSCYSDD7 - 18527 - 205
774PROPROAA8 - 18428 - 204
884PROPROEE8 - 18428 - 204
995PROPROAA8 - 18428 - 204
10105PROPROFF8 - 18428 - 204
11116PROPROAA8 - 18428 - 204
12126PROPROGG8 - 18428 - 204
13137PROPROAA8 - 18428 - 204
14147PROPROHH8 - 18428 - 204
15158CYSCYSBB8 - 18528 - 205
16168CYSCYSCC8 - 18528 - 205
17179PROPROBB8 - 18428 - 204
18189PROPRODD8 - 18428 - 204
191910CYSCYSBB8 - 18528 - 205
202010CYSCYSEE8 - 18528 - 205
212111CYSCYSBB8 - 18528 - 205
222211CYSCYSFF8 - 18528 - 205
232312CYSCYSBB8 - 18528 - 205
242412CYSCYSGG8 - 18528 - 205
252513CYSCYSBB8 - 18528 - 205
262613CYSCYSHH8 - 18528 - 205
272714PROPROCC8 - 18428 - 204
282814PROPRODD8 - 18428 - 204
292915CYSCYSCC8 - 18528 - 205
303015CYSCYSEE8 - 18528 - 205
313116CYSCYSCC8 - 18528 - 205
323216CYSCYSFF8 - 18528 - 205
333317CYSCYSCC8 - 18528 - 205
343417CYSCYSGG8 - 18528 - 205
353518CYSCYSCC8 - 18528 - 205
363618CYSCYSHH8 - 18528 - 205
373719PROPRODD8 - 18428 - 204
383819PROPROEE8 - 18428 - 204
393920PROPRODD8 - 18428 - 204
404020PROPROFF8 - 18428 - 204
414121PROPRODD8 - 18428 - 204
424221PROPROGG8 - 18428 - 204
434322PROPRODD8 - 18428 - 204
444422PROPROHH8 - 18428 - 204
454523CYSCYSEE8 - 18528 - 205
464623CYSCYSFF8 - 18528 - 205
474724CYSCYSEE8 - 18528 - 205
484824CYSCYSGG8 - 18528 - 205
494925CYSCYSEE8 - 18528 - 205
505025CYSCYSHH8 - 18528 - 205
515126CYSCYSFF8 - 18528 - 205
525226CYSCYSGG8 - 18528 - 205
535327CYSCYSFF8 - 18528 - 205
545427CYSCYSHH8 - 18528 - 205
555528CYSCYSGG8 - 18528 - 205
565628CYSCYSHH8 - 18528 - 205

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
Acetyltransferase / Ribosomal-protein-alanine N-acetyltransferase / Streptothricin acetyltransferase


Mass: 22071.469 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lavendulae subsp. lavendulae (bacteria)
Gene: SLAV_37450 / Production host: Escherichia coli (E. coli) / References: UniProt: G9MBU1
#2: Chemical
ChemComp-OI9 / Streptothricin F


Mass: 502.522 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C19H34N8O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5 0.2 M ammonium sulfate 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.415→20 Å / Num. obs: 59578 / % possible obs: 97.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.099 / Net I/σ(I): 15.2
Reflection shellResolution: 2.42→2.51 Å / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 5876 / Rrim(I) all: 0.545

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PP9
Resolution: 2.415→19.899 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.252 / SU ML: 0.189 / Cross valid method: FREE R-VALUE / ESU R: 0.501 / ESU R Free: 0.27
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2454 2912 4.888 %
Rwork0.2114 56666 -
all0.213 --
obs-59578 96.958 %
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: 34.404 Å2
Baniso -1Baniso -2Baniso -3
1-1.657 Å20.287 Å2-0.235 Å2
2---0.04 Å20.424 Å2
3----1.615 Å2
Refinement stepCycle: LAST / Resolution: 2.415→19.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10302 0 280 537 11119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01310830
X-RAY DIFFRACTIONr_bond_other_d0.0030.01810004
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.68214748
X-RAY DIFFRACTIONr_angle_other_deg1.2251.6322916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17651354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.78220.137584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.898151482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.01115104
X-RAY DIFFRACTIONr_chiral_restr0.0670.21428
X-RAY DIFFRACTIONr_chiral_restr_other1.2320.264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022634
X-RAY DIFFRACTIONr_nbd_refined0.1730.21863
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.29260
X-RAY DIFFRACTIONr_nbtor_refined0.1570.25224
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.25113
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2561
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0870.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.241
X-RAY DIFFRACTIONr_nbd_other0.2210.2113
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.28
X-RAY DIFFRACTIONr_mcbond_it1.7113.565488
X-RAY DIFFRACTIONr_mcbond_other1.713.565488
X-RAY DIFFRACTIONr_mcangle_it2.8865.3266818
X-RAY DIFFRACTIONr_mcangle_other2.8855.3266819
X-RAY DIFFRACTIONr_scbond_it1.9383.7795342
X-RAY DIFFRACTIONr_scbond_other1.9373.7795343
X-RAY DIFFRACTIONr_scangle_it3.3095.5627930
X-RAY DIFFRACTIONr_scangle_other3.3095.5627931
X-RAY DIFFRACTIONr_lrange_it5.35741.04511489
X-RAY DIFFRACTIONr_lrange_other5.3140.93111394
X-RAY DIFFRACTIONr_ncsr_local_group_10.0560.054986
X-RAY DIFFRACTIONr_ncsr_local_group_20.0690.054970
X-RAY DIFFRACTIONr_ncsr_local_group_30.0370.055103
X-RAY DIFFRACTIONr_ncsr_local_group_40.0370.055063
X-RAY DIFFRACTIONr_ncsr_local_group_50.0530.054977
X-RAY DIFFRACTIONr_ncsr_local_group_60.0560.054968
X-RAY DIFFRACTIONr_ncsr_local_group_70.0320.055057
X-RAY DIFFRACTIONr_ncsr_local_group_80.0510.055074
X-RAY DIFFRACTIONr_ncsr_local_group_90.0540.054985
X-RAY DIFFRACTIONr_ncsr_local_group_100.0480.055023
X-RAY DIFFRACTIONr_ncsr_local_group_110.0330.055078
X-RAY DIFFRACTIONr_ncsr_local_group_120.0520.055054
X-RAY DIFFRACTIONr_ncsr_local_group_130.0490.055022
X-RAY DIFFRACTIONr_ncsr_local_group_140.0670.054995
X-RAY DIFFRACTIONr_ncsr_local_group_150.0630.055006
X-RAY DIFFRACTIONr_ncsr_local_group_160.0520.055063
X-RAY DIFFRACTIONr_ncsr_local_group_170.0640.055059
X-RAY DIFFRACTIONr_ncsr_local_group_180.070.054999
X-RAY DIFFRACTIONr_ncsr_local_group_190.0330.055064
X-RAY DIFFRACTIONr_ncsr_local_group_200.0520.054974
X-RAY DIFFRACTIONr_ncsr_local_group_210.0540.054963
X-RAY DIFFRACTIONr_ncsr_local_group_220.0280.055053
X-RAY DIFFRACTIONr_ncsr_local_group_230.0530.055004
X-RAY DIFFRACTIONr_ncsr_local_group_240.0570.054995
X-RAY DIFFRACTIONr_ncsr_local_group_250.0310.055092
X-RAY DIFFRACTIONr_ncsr_local_group_260.0480.055053
X-RAY DIFFRACTIONr_ncsr_local_group_270.0530.054997
X-RAY DIFFRACTIONr_ncsr_local_group_280.0560.054988
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.055640.0501
12BX-RAY DIFFRACTIONLocal ncs0.055640.0501
23AX-RAY DIFFRACTIONLocal ncs0.069060.0501
24CX-RAY DIFFRACTIONLocal ncs0.069060.0501
35AX-RAY DIFFRACTIONLocal ncs0.036740.05011
36DX-RAY DIFFRACTIONLocal ncs0.036740.05011
47AX-RAY DIFFRACTIONLocal ncs0.03680.05011
48EX-RAY DIFFRACTIONLocal ncs0.03680.05011
59AX-RAY DIFFRACTIONLocal ncs0.05340.0501
510FX-RAY DIFFRACTIONLocal ncs0.05340.0501
611AX-RAY DIFFRACTIONLocal ncs0.055630.0501
612GX-RAY DIFFRACTIONLocal ncs0.055630.0501
713AX-RAY DIFFRACTIONLocal ncs0.031610.05011
714HX-RAY DIFFRACTIONLocal ncs0.031610.05011
815BX-RAY DIFFRACTIONLocal ncs0.050570.05011
816CX-RAY DIFFRACTIONLocal ncs0.050570.05011
917BX-RAY DIFFRACTIONLocal ncs0.054390.0501
918DX-RAY DIFFRACTIONLocal ncs0.054390.0501
1019BX-RAY DIFFRACTIONLocal ncs0.048260.0501
1020EX-RAY DIFFRACTIONLocal ncs0.048260.0501
1121BX-RAY DIFFRACTIONLocal ncs0.033350.05011
1122FX-RAY DIFFRACTIONLocal ncs0.033350.05011
1223BX-RAY DIFFRACTIONLocal ncs0.051860.05011
1224GX-RAY DIFFRACTIONLocal ncs0.051860.05011
1325BX-RAY DIFFRACTIONLocal ncs0.049220.0501
1326HX-RAY DIFFRACTIONLocal ncs0.049220.0501
1427CX-RAY DIFFRACTIONLocal ncs0.067280.0501
1428DX-RAY DIFFRACTIONLocal ncs0.067280.0501
1529CX-RAY DIFFRACTIONLocal ncs0.06260.0501
1530EX-RAY DIFFRACTIONLocal ncs0.06260.0501
1631CX-RAY DIFFRACTIONLocal ncs0.051610.05011
1632FX-RAY DIFFRACTIONLocal ncs0.051610.05011
1733CX-RAY DIFFRACTIONLocal ncs0.063650.05011
1734GX-RAY DIFFRACTIONLocal ncs0.063650.05011
1835CX-RAY DIFFRACTIONLocal ncs0.069560.0501
1836HX-RAY DIFFRACTIONLocal ncs0.069560.0501
1937DX-RAY DIFFRACTIONLocal ncs0.033010.05011
1938EX-RAY DIFFRACTIONLocal ncs0.033010.05011
2039DX-RAY DIFFRACTIONLocal ncs0.052070.0501
2040FX-RAY DIFFRACTIONLocal ncs0.052070.0501
2141DX-RAY DIFFRACTIONLocal ncs0.054480.0501
2142GX-RAY DIFFRACTIONLocal ncs0.054480.0501
2243DX-RAY DIFFRACTIONLocal ncs0.028350.05011
2244HX-RAY DIFFRACTIONLocal ncs0.028350.05011
2345EX-RAY DIFFRACTIONLocal ncs0.052790.0501
2346FX-RAY DIFFRACTIONLocal ncs0.052790.0501
2447EX-RAY DIFFRACTIONLocal ncs0.057260.0501
2448GX-RAY DIFFRACTIONLocal ncs0.057260.0501
2549EX-RAY DIFFRACTIONLocal ncs0.030840.05011
2550HX-RAY DIFFRACTIONLocal ncs0.030840.05011
2651FX-RAY DIFFRACTIONLocal ncs0.048480.05011
2652GX-RAY DIFFRACTIONLocal ncs0.048480.05011
2753FX-RAY DIFFRACTIONLocal ncs0.052990.0501
2754HX-RAY DIFFRACTIONLocal ncs0.052990.0501
2855GX-RAY DIFFRACTIONLocal ncs0.056450.0501
2856HX-RAY DIFFRACTIONLocal ncs0.056450.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.415-2.4770.2751700.2563768X-RAY DIFFRACTION86.9508
2.477-2.5450.3012190.2574138X-RAY DIFFRACTION97.5375
2.545-2.6180.3252110.2593848X-RAY DIFFRACTION97.5956
2.618-2.6980.2862080.2473934X-RAY DIFFRACTION97.4588
2.698-2.7860.2931840.253733X-RAY DIFFRACTION97.6078
2.786-2.8820.3341920.2333635X-RAY DIFFRACTION97.8022
2.882-2.990.2341980.2133480X-RAY DIFFRACTION97.6633
2.99-3.1110.2832060.2133291X-RAY DIFFRACTION97.1119
3.111-3.2480.2581860.2253262X-RAY DIFFRACTION97.8156
3.248-3.4040.2761770.2073057X-RAY DIFFRACTION97.6155
3.404-3.5860.2771030.2092968X-RAY DIFFRACTION98.0524
3.586-3.80.2111560.1982779X-RAY DIFFRACTION97.8333
3.8-4.0580.2181410.1912672X-RAY DIFFRACTION98.2193
4.058-4.3760.2041440.1842423X-RAY DIFFRACTION98.617
4.376-4.7840.18970.1732286X-RAY DIFFRACTION98.9207
4.784-5.3310.208960.1792075X-RAY DIFFRACTION99.042
5.331-6.1240.221710.1981879X-RAY DIFFRACTION99.1357
6.124-7.4230.231570.2021544X-RAY DIFFRACTION99.0105
7.423-10.1910.219470.1991249X-RAY DIFFRACTION98.7805

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