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- PDB-2mzz: NMR structure of APOBEC3G NTD variant, sNTD -

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Basic information

Entry
Database: PDB / ID: 2mzz
TitleNMR structure of APOBEC3G NTD variant, sNTD
ComponentsApolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G variant
KeywordsHydrolase / Antiviral protein / Vif-binding domain
Biological speciesartificial gene (others)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsKouno, T. / Luengas, E.M. / Shigematu, M. / Shandilya, S.M.D. / Zhang, J. / Chen, L. / Hara, M. / Schiffer, C.A. / Harris, R.S. / Matsuo, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structure of the Vif-binding domain of the antiviral enzyme APOBEC3G.
Authors: Kouno, T. / Luengas, E.M. / Shigematsu, M. / Shandilya, S.M. / Zhang, J. / Chen, L. / Hara, M. / Schiffer, C.A. / Harris, R.S. / Matsuo, H.
History
DepositionFeb 28, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jul 1, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / 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_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3812
Polymers21,3161
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G variant


Mass: 21316.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N TROSY
1223D HNCA-TROSY
1323D HN(CO)CA-TROSY
1423D HNCO-TROSY
1523D HN(CA)CO-TROSY
1623D HN(CA)CB-TROSY
1723D HN(CO)CACB-TROSY
1833D 15N-edited NOESY
1942D 1H-15N TROSY
11052D 1H-15N TROSY
11162D 1H-15N TROSY
11272D 1H-15N TROSY
11382D 1H-15N TROSY
11492D 1H-15N TROSY
115102D 1H-13C HSQC
116112D 1H-13C HSQC
117122D 1H-13C HSQC
118132D 1H-13C HSQC
119142D 1H-13C HSQC
120152D 1H-13C HSQC
121162D 1H-13C HSQC
122172D 1H-13C HSQC
123182D 1H-13C HSQC
124192D 1H-13C HSQC
125102D 1H-1H NOESY
126112D 1H-1H NOESY
127122D 1H-1H NOESY
128132D 1H-1H NOESY
129142D 1H-1H NOESY
130152D 1H-1H NOESY
131162D 1H-1H NOESY
132172D 1H-1H NOESY
133182D 1H-1H NOESY
134192D 1H-1H NOESY
135202D 1H-1H NOESY
136212D 1H-1H NOESY
137222D 1H-1H NOESY
138232D 1H-1H NOESY
139242D 1H-1H NOESY
14033D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.15-0.20 mM [U-100% 15N; U-85% 2H] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 95% H2O/5% D2O95% H2O/5% D2O
20.15-0.20 mM [U-100% 13C; U-100% 15N; U-85% 2H] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 95% H2O/5% D2O95% H2O/5% D2O
30.05-0.10 mM [U-100% 13C; U-100% 15N; U-60% 2H] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 95% H2O/5% D2O95% H2O/5% D2O
40.05-0.10 mM [U-80% 2H; 100% 15N-Arg] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 95% H2O/5% D2O95% H2O/5% D2O
50.05-0.10 mM [U-80% 2H; 100% 15N-Ile] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 95% H2O/5% D2O95% H2O/5% D2O
60.05-0.10 mM [U-80% 2H; 100% 15N-Leu] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 95% H2O/5% D2O95% H2O/5% D2O
70.05-0.10 mM [U-80% 2H; 100% 15N-Lys] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 95% H2O/5% D2O95% H2O/5% D2O
80.05-0.10 mM [U-80% 2H; 100% 15N-Phe] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 95% H2O/5% D2O95% H2O/5% D2O
90.05-0.10 mM [U-80% 2H; 100% 15N-Tyr] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 95% H2O/5% D2O95% H2O/5% D2O
100.05-0.10 mM [U-80% 2H; 100% 1H, 100% 13C-Ala] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
110.05-0.10 mM [U-80% 2H; 100% 1H, 100% 13C-Arg] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
120.05-0.10 mM [U-80% 2H; 100% 1H, 100% 13C-Ile] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
130.05-0.10 mM [U-80% 2H; 100% 1H, 100% 13C-Leu] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
140.05-0.10 mM [U-80% 2H; 100% 1H, 100% 13C-Lys] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
150.05-0.10 mM [U-80% 2H; 100% 1H, 100% 13C-Met] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
160.05-0.10 mM [U-80% 2H; 100% 1H, 100% 13C-Phe] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
170.05-0.10 mM [U-80% 2H; 100% 1H, 100% 13C-Thr] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
180.05-0.10 mM [U-80% 2H; 100% 1H, 100% 13C-Tyr] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
190.05-0.10 mM [U-80% 2H; 100% 1H, 100% 13C-Val] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
200.05-0.10 mM [U-80% 2H; 100% 1H-Phe,Tyr,Ile] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
210.05-0.10 mM [U-80% 2H; 100% 1H-Phe,Tyr,Leu] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
220.05-0.10 mM [U-80% 2H; 100% 1H-Phe,Tyr,Val] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
230.05-0.10 mM [U-80% 2H; 100% 1H-Trp,Ile,Leu,Val] sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
240.15-0.20 mM sNTD, 10 mM sodium phosphate, 100 mM sodium chloride, 0.005 % Tween 20, 0.5 mM TCEP, 0.01 % sodium azide, 0.5 M [U-98% 2H] Choline o-sulfate, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMsNTD-1[U-100% 15N; U-85% 2H]0.15-0.201
10 mMsodium phosphate-21
100 mMsodium chloride-31
0.005 %Tween 20-41
0.5 mMTCEP-51
0.01 %sodium azide-61
0.5 MCholine o-sulfate-7[U-98% 2H]1
mMsNTD-8[U-100% 13C; U-100% 15N; U-85% 2H]0.15-0.202
10 mMsodium phosphate-92
100 mMsodium chloride-102
0.005 %Tween 20-112
0.5 mMTCEP-122
0.01 %sodium azide-132
0.5 MCholine o-sulfate-14[U-98% 2H]2
mMsNTD-15[U-100% 13C; U-100% 15N; U-60% 2H]0.05-0.103
10 mMsodium phosphate-163
100 mMsodium chloride-173
0.005 %Tween 20-183
0.5 mMTCEP-193
0.01 %sodium azide-203
0.5 MCholine o-sulfate-21[U-98% 2H]3
mMsNTD-22[U-80% 2H; 100% 15N-Arg]0.05-0.104
10 mMsodium phosphate-234
100 mMsodium chloride-244
0.005 %Tween 20-254
0.5 mMTCEP-264
0.01 %sodium azide-274
0.5 MCholine o-sulfate-28[U-98% 2H]4
mMsNTD-29[U-80% 2H; 100% 15N-Ile]0.05-0.105
10 mMsodium phosphate-305
100 mMsodium chloride-315
0.005 %Tween 20-325
0.5 mMTCEP-335
0.01 %sodium azide-345
0.5 MCholine o-sulfate-35[U-98% 2H]5
mMsNTD-36[U-80% 2H; 100% 15N-Leu]0.05-0.106
10 mMsodium phosphate-376
100 mMsodium chloride-386
0.005 %Tween 20-396
0.5 mMTCEP-406
0.01 %sodium azide-416
0.5 MCholine o-sulfate-42[U-98% 2H]6
mMsNTD-43[U-80% 2H; 100% 15N-Lys]0.05-0.107
10 mMsodium phosphate-447
100 mMsodium chloride-457
0.005 %Tween 20-467
0.5 mMTCEP-477
0.01 %sodium azide-487
0.5 MCholine o-sulfate-49[U-98% 2H]7
mMsNTD-50[U-80% 2H; 100% 15N-Phe]0.05-0.108
10 mMsodium phosphate-518
100 mMsodium chloride-528
0.005 %Tween 20-538
0.5 mMTCEP-548
0.01 %sodium azide-558
0.5 MCholine o-sulfate-56[U-98% 2H]8
mMsNTD-57[U-80% 2H; 100% 15N-Tyr]0.05-0.109
10 mMsodium phosphate-589
100 mMsodium chloride-599
0.005 %Tween 20-609
0.5 mMTCEP-619
0.01 %sodium azide-629
0.5 MCholine o-sulfate-63[U-98% 2H]9
mMsNTD-64[U-80% 2H; 100% 1H, 100% 13C-Ala]0.05-0.1010
10 mMsodium phosphate-6510
100 mMsodium chloride-6610
0.005 %Tween 20-6710
0.5 mMTCEP-6810
0.01 %sodium azide-6910
0.5 MCholine o-sulfate-70[U-98% 2H]10
mMsNTD-71[U-80% 2H; 100% 1H, 100% 13C-Arg]0.05-0.1011
10 mMsodium phosphate-7211
100 mMsodium chloride-7311
0.005 %Tween 20-7411
0.5 mMTCEP-7511
0.01 %sodium azide-7611
0.5 MCholine o-sulfate-77[U-98% 2H]11
mMsNTD-78[U-80% 2H; 100% 1H, 100% 13C-Ile]0.05-0.1012
10 mMsodium phosphate-7912
100 mMsodium chloride-8012
0.005 %Tween 20-8112
0.5 mMTCEP-8212
0.01 %sodium azide-8312
0.5 MCholine o-sulfate-84[U-98% 2H]12
mMsNTD-85[U-80% 2H; 100% 1H, 100% 13C-Leu]0.05-0.1013
10 mMsodium phosphate-8613
100 mMsodium chloride-8713
0.005 %Tween 20-8813
0.5 mMTCEP-8913
0.01 %sodium azide-9013
0.5 MCholine o-sulfate-91[U-98% 2H]13
mMsNTD-92[U-80% 2H; 100% 1H, 100% 13C-Lys]0.05-0.1014
10 mMsodium phosphate-9314
100 mMsodium chloride-9414
0.005 %Tween 20-9514
0.5 mMTCEP-9614
0.01 %sodium azide-9714
0.5 MCholine o-sulfate-98[U-98% 2H]14
mMsNTD-99[U-80% 2H; 100% 1H, 100% 13C-Met]0.05-0.1015
10 mMsodium phosphate-10015
100 mMsodium chloride-10115
0.005 %Tween 20-10215
0.5 mMTCEP-10315
0.01 %sodium azide-10415
0.5 MCholine o-sulfate-105[U-98% 2H]15
mMsNTD-106[U-80% 2H; 100% 1H, 100% 13C-Phe]0.05-0.1016
10 mMsodium phosphate-10716
100 mMsodium chloride-10816
0.005 %Tween 20-10916
0.5 mMTCEP-11016
0.01 %sodium azide-11116
0.5 MCholine o-sulfate-112[U-98% 2H]16
mMsNTD-113[U-80% 2H; 100% 1H, 100% 13C-Thr]0.05-0.1017
10 mMsodium phosphate-11417
100 mMsodium chloride-11517
0.005 %Tween 20-11617
0.5 mMTCEP-11717
0.01 %sodium azide-11817
0.5 MCholine o-sulfate-119[U-98% 2H]17
mMsNTD-120[U-80% 2H; 100% 1H, 100% 13C-Tyr]0.05-0.1018
10 mMsodium phosphate-12118
100 mMsodium chloride-12218
0.005 %Tween 20-12318
0.5 mMTCEP-12418
0.01 %sodium azide-12518
0.5 MCholine o-sulfate-126[U-98% 2H]18
mMsNTD-127[U-80% 2H; 100% 1H, 100% 13C-Val]0.05-0.1019
10 mMsodium phosphate-12819
100 mMsodium chloride-12919
0.005 %Tween 20-13019
0.5 mMTCEP-13119
0.01 %sodium azide-13219
0.5 MCholine o-sulfate-133[U-98% 2H]19
mMsNTD-134[U-80% 2H; 100% 1H-Phe,Tyr,Ile]0.05-0.1020
10 mMsodium phosphate-13520
100 mMsodium chloride-13620
0.005 %Tween 20-13720
0.5 mMTCEP-13820
0.01 %sodium azide-13920
0.5 MCholine o-sulfate-140[U-98% 2H]20
mMsNTD-141[U-80% 2H; 100% 1H-Phe,Tyr,Leu]0.05-0.1021
10 mMsodium phosphate-14221
100 mMsodium chloride-14321
0.005 %Tween 20-14421
0.5 mMTCEP-14521
0.01 %sodium azide-14621
0.5 MCholine o-sulfate-147[U-98% 2H]21
mMsNTD-148[U-80% 2H; 100% 1H-Phe,Tyr,Val]0.05-0.1022
10 mMsodium phosphate-14922
100 mMsodium chloride-15022
0.005 %Tween 20-15122
0.5 mMTCEP-15222
0.01 %sodium azide-15322
0.5 MCholine o-sulfate-154[U-98% 2H]22
mMsNTD-155[U-80% 2H; 100% 1H-Trp,Ile,Leu,Val]0.05-0.1023
10 mMsodium phosphate-15623
100 mMsodium chloride-15723
0.005 %Tween 20-15823
0.5 mMTCEP-15923
0.01 %sodium azide-16023
0.5 MCholine o-sulfate-161[U-98% 2H]23
mMsNTD-1620.15-0.2024
10 mMsodium phosphate-16324
100 mMsodium chloride-16424
0.005 %Tween 20-16524
0.5 mMTCEP-16624
0.01 %sodium azide-16724
0.5 MCholine o-sulfate-168[U-98% 2H]24
Sample conditionspH: 7.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8502
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxestimation of dihedral angles
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
MOLMOLKoradi, Billeter and Wuthrichdrawing structures
MacPyMolSchrodingerdrawing structures
ProcheckNMRLaskowski and MacArthurevaluation of structure quality
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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