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- PDB-3ztr: Hexagonal form P6122 of the Aquifex aeolicus nucleoside diphospha... -

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Basic information

Entry
Database: PDB / ID: 3ztr
TitleHexagonal form P6122 of the Aquifex aeolicus nucleoside diphosphate kinase (FIRST STAGE OF RADIATION DAMAGE)
ComponentsNUCLEOSIDE DIPHOSPHATE KINASENucleoside-diphosphate kinase
KeywordsTRANSFERASE / NUCLEOSIDE DIPHOSPHATE KINASE / DISULFIDE BRIDGE
Function / homology
Function and homology information


purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinases active site. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBoissier, F. / Georgescauld, F. / Moynie, L. / Dupuy, J.-W. / Sarger, C. / Podar, M. / Lascu, I. / Giraud, M.-F. / Dautant, A.
Citation
Journal: Proteins / Year: 2012
Title: An Inter-Subunit Disulphide Bridge Stabilizes the Tetrameric Nucleoside Diphosphate Kinase of Aquifex Aeolicus
Authors: Boissier, F. / Georgescauld, F. / Moynie, L. / Dupuy, J.-W. / Sarger, C. / Podar, M. / Lascu, L. / Giraud, M.-F. / Dautant, A.
#1: Journal: Proteins / Year: 2007
Title: The Structure of the Escherichia Coli Nucleoside Diphosphate Kinase Reveals a New Quaternary Architecture for This Enzyme Family.
Authors: Moynie, L. / Giraud, M. / Georgescauld, F. / Lascu, I. / Dautant, A.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystal Structure of Myxococcus Xanthus Nucleoside Diphosphate Kinase and its Interaction with a Nucleotide Substrate at 2.0 A Resolution.
Authors: Williams, R.L. / Oren, D.A. / Munoz-Dorado, J. / Inouye, S. / Inouye, M. / Arnold, E.
History
DepositionJul 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
C: NUCLEOSIDE DIPHOSPHATE KINASE
D: NUCLEOSIDE DIPHOSPHATE KINASE
E: NUCLEOSIDE DIPHOSPHATE KINASE
F: NUCLEOSIDE DIPHOSPHATE KINASE
G: NUCLEOSIDE DIPHOSPHATE KINASE
H: NUCLEOSIDE DIPHOSPHATE KINASE
I: NUCLEOSIDE DIPHOSPHATE KINASE
J: NUCLEOSIDE DIPHOSPHATE KINASE
K: NUCLEOSIDE DIPHOSPHATE KINASE
L: NUCLEOSIDE DIPHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)191,56012
Polymers191,56012
Non-polymers00
Water19,1141061
1
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
C: NUCLEOSIDE DIPHOSPHATE KINASE
D: NUCLEOSIDE DIPHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)63,8534
Polymers63,8534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-43.8 kcal/mol
Surface area24850 Å2
MethodPISA
2
E: NUCLEOSIDE DIPHOSPHATE KINASE
F: NUCLEOSIDE DIPHOSPHATE KINASE
G: NUCLEOSIDE DIPHOSPHATE KINASE
H: NUCLEOSIDE DIPHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)63,8534
Polymers63,8534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-43.5 kcal/mol
Surface area24810 Å2
MethodPISA
3
I: NUCLEOSIDE DIPHOSPHATE KINASE
J: NUCLEOSIDE DIPHOSPHATE KINASE
K: NUCLEOSIDE DIPHOSPHATE KINASE
L: NUCLEOSIDE DIPHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)63,8534
Polymers63,8534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-44.1 kcal/mol
Surface area24820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.710, 200.710, 246.731
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-2067-

HOH

21B-2091-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
12
22
32
42
52
62
13
23
33
43
53
63

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND RESID 2:142 AND BACKBONE
211CHAIN B AND RESID 2:142 AND BACKBONE
311CHAIN C AND RESID 2:142 AND BACKBONE
411CHAIN D AND RESID 2:142 AND BACKBONE
511CHAIN E AND RESID 2:142 AND BACKBONE
611CHAIN F AND RESID 2:142 AND BACKBONE
711CHAIN G AND RESID 2:142 AND BACKBONE
811CHAIN H AND RESID 2:142 AND BACKBONE
911CHAIN I AND RESID 2:142 AND BACKBONE
1011CHAIN J AND RESID 2:142 AND BACKBONE
1111CHAIN K AND RESID 2:142 AND BACKBONE
1211CHAIN L AND RESID 2:142 AND BACKBONE
112CHAIN A AND SIDECHAIN AND RESSEQ 2:142 AND NOT (RESSEQ 96 OR RESSEQ 114)
212CHAIN B AND SIDECHAIN AND RESSEQ 2:142 AND NOT (RESSEQ 96 OR RESSEQ 114)
312CHAIN E AND SIDECHAIN AND RESSEQ 2:142 AND NOT (RESSEQ 96 OR RESSEQ 114)
412CHAIN F AND SIDECHAIN AND RESSEQ 2:142 AND NOT (RESSEQ 96 OR RESSEQ 114)
512CHAIN I AND SIDECHAIN AND RESSEQ 2:142 AND NOT (RESSEQ 96 OR RESSEQ 114)
612CHAIN J AND SIDECHAIN AND RESSEQ 2:142 AND NOT (RESSEQ 96 OR RESSEQ 114)
113CHAIN C AND SIDECHAIN AND RESSEQ 2:142 AND NOT (RESSEQ 96 OR RESSEQ 100 OR RESSEQ 114)
213CHAIN D AND SIDECHAIN AND RESSEQ 2:142 AND NOT (RESSEQ 96 OR RESSEQ 100 OR RESSEQ 114)
313CHAIN G AND SIDECHAIN AND RESSEQ 2:142 AND NOT (RESSEQ 96 OR RESSEQ 100 OR RESSEQ 114)
413CHAIN H AND SIDECHAIN AND RESSEQ 2:142 AND NOT (RESSEQ 96 OR RESSEQ 100 OR RESSEQ 114)
513CHAIN K AND SIDECHAIN AND RESSEQ 2:142 AND NOT (RESSEQ 96 OR RESSEQ 100 OR RESSEQ 114)
613CHAIN L AND SIDECHAIN AND RESSEQ 2:142 AND NOT (RESSEQ 96 OR RESSEQ 100 OR RESSEQ 114)

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
NUCLEOSIDE DIPHOSPHATE KINASE / Nucleoside-diphosphate kinase / NDK / NDP KINASE / NUCLEOSIDE-2-P KINASE


Mass: 15963.325 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67528, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1061 / Source method: isolated from a natural source / Formula: H2O

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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: 3.75 Å3/Da / Density % sol: 67.2 % / Description: NONE
Crystal growpH: 5.5 / Details: 25% PEG 3350, 0.2 M NACL, 0.1 M BIS-TRIS PH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2008 / Details: KIRKPATRICK BAEZ
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→52.44 Å / Num. obs: 221854 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Biso Wilson estimate: 18.39 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.6 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZTO
Resolution: 2.3→52.444 Å / SU ML: 0.28 / σ(F): 0.49 / Phase error: 25.9 / Stereochemistry target values: ML
Details: IN THE SSBOND CARDS: THE FIRST ATOM BELONGS TO THE ALTERNATE CONFORMER A (WITH OCCUPANCY Q1). THE SECOND ONE BELONGS TO THE ALTERNATE CONFORMER B (WITH OCCUPANCY Q2). ABS(Q1 - Q2)*100 IS THE ...Details: IN THE SSBOND CARDS: THE FIRST ATOM BELONGS TO THE ALTERNATE CONFORMER A (WITH OCCUPANCY Q1). THE SECOND ONE BELONGS TO THE ALTERNATE CONFORMER B (WITH OCCUPANCY Q2). ABS(Q1 - Q2)*100 IS THE PERCENTAGE OF CYS133 NOT INVOLVED IN THE DISULFIDE BRIDGE.
RfactorNum. reflection% reflection
Rfree0.22 11149 5 %
Rwork0.1915 --
obs0.1929 221854 89.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.445 Å2 / ksol: 0.392 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.9956 Å20 Å20 Å2
2--0.9956 Å20 Å2
3----1.9912 Å2
Refinement stepCycle: LAST / Resolution: 2.3→52.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13380 0 0 1061 14441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01213731
X-RAY DIFFRACTIONf_angle_d1.21418489
X-RAY DIFFRACTIONf_dihedral_angle_d15.035247
X-RAY DIFFRACTIONf_chiral_restr0.0841995
X-RAY DIFFRACTIONf_plane_restr0.0052448
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A565X-RAY DIFFRACTIONPOSITIONAL
12B565X-RAY DIFFRACTIONPOSITIONAL0.025
13C563X-RAY DIFFRACTIONPOSITIONAL0.035
14D564X-RAY DIFFRACTIONPOSITIONAL0.035
15E565X-RAY DIFFRACTIONPOSITIONAL0.029
16F563X-RAY DIFFRACTIONPOSITIONAL0.024
17G564X-RAY DIFFRACTIONPOSITIONAL0.035
18H563X-RAY DIFFRACTIONPOSITIONAL0.028
19I564X-RAY DIFFRACTIONPOSITIONAL0.032
110J565X-RAY DIFFRACTIONPOSITIONAL0.028
111K563X-RAY DIFFRACTIONPOSITIONAL0.036
112L565X-RAY DIFFRACTIONPOSITIONAL0.031
21A543X-RAY DIFFRACTIONPOSITIONAL
22B543X-RAY DIFFRACTIONPOSITIONAL0.058
23E543X-RAY DIFFRACTIONPOSITIONAL0.091
24F539X-RAY DIFFRACTIONPOSITIONAL0.052
25I538X-RAY DIFFRACTIONPOSITIONAL0.065
26J543X-RAY DIFFRACTIONPOSITIONAL0.065
31C529X-RAY DIFFRACTIONPOSITIONAL
32D529X-RAY DIFFRACTIONPOSITIONAL0.057
33G529X-RAY DIFFRACTIONPOSITIONAL0.06
34H536X-RAY DIFFRACTIONPOSITIONAL0.092
35K536X-RAY DIFFRACTIONPOSITIONAL0.053
36L534X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.285711150.248721661X-RAY DIFFRACTION92
2.3822-2.47760.2711550.235521576X-RAY DIFFRACTION92
2.4776-2.59040.25111020.21821629X-RAY DIFFRACTION92
2.5904-2.72690.236912420.206121350X-RAY DIFFRACTION92
2.7269-2.89780.237111180.201821425X-RAY DIFFRACTION91
2.8978-3.12150.22610950.194821213X-RAY DIFFRACTION90
3.1215-3.43550.205710870.184921157X-RAY DIFFRACTION90
3.4355-3.93250.205511110.172721291X-RAY DIFFRACTION91
3.9325-4.9540.161610460.144520296X-RAY DIFFRACTION86
4.954-52.45750.212210780.186819107X-RAY DIFFRACTION82
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)
10.5566-0.3476-0.27340.39070.14620.1499-0.1046-0.1355-0.08690.14450.0607-0.01680.04140.01470.01730.04530.0474-0.00950.09780.01050.039236.3475-76.1254-2.1538
20.2097-0.1156-0.60450.0830.412.0584-0.0013-0.1534-0.04030.03410.11940.1043-0.25760.1316-0.10290.25230.08510.06750.53540.20320.240831.8743-89.97027.5228
30.132-0.10470.14860.7283-0.30040.76170.04530.06390.0042-0.1702-0.0629-0.02-0.11540.1390.0390.04630.05-0-0.01760.01090.021747.9388-69.485-23.9534
40.0188-0.0377-0.08760.09170.18771.69070.0198-0.02880.0533-0.14410.1778-0.0674-0.1482-0.0652-0.18740.5362-0.03770.22650.4308-0.02630.097161.9739-72.6403-33.8264
50.8521-0.54410.36450.4901-0.14020.4781-0.0654-0.068-0.01740.06180.00950.01950.08860.13330.04390.07910.0704-0.00120.10960.01760.056163.8511-95.6831-2.8859
60.0275-0.0434-0.08780.07040.14040.282-0.086-0.05510.05040.00850.0018-0.0026-0.1329-0.10240.08250.39460.2231-0.20630.3586-0.17230.267268.6834-81.59586.2158
70.3411-0.1664-0.00650.73320.54030.59860.03190.1175-0.0465-0.0573-0.05530.05640.16620.00530.01970.09610.0436-0.00630.0648-0.00680.054450.8262-103.0462-23.663
80.12850.06610.35210.082-0.03592.07290.01750.0755-0.0532-0.01860.06930.0484-0.1476-0.0032-0.07360.4110.0676-0.09050.40080.01240.302136.1194-99.9999-32.5473
90.48320.1790.50810.4050.09920.61220.052-0.1198-0.00470.0043-0.03410.1023-0.063-0.01510.01770.0074-0.0143-0.00240.0972-0.01870.042815.1856-50.8437-16.2405
100.15830.0129-0.13820.04010.08960.38880.22650.02020.0667-0.0624-0.0396-0.0274-0.27310.0889-0.17720.3307-0.03540.10020.4679-0.21210.23795.2394-40.3819-6.4103
110.06690.1598-0.10070.7256-0.10090.31770.01820.08130.041-0.04160.01170.165-0.0113-0.09350.0190.00380.0186-0.0190.0667-0.01260.007815.3993-64.3465-37.9482
121.0714-0.4323-1.530.190.44134.18220.31480.0825-0.12-0.0308-0.1699-0.0526-0.3642-0.3641-0.12680.32070.0969-0.0910.36-0.14720.16235.7844-75.3381-47.5491
131.1270.2398-0.21890.3853-0.07160.3006-0.0379-0.20910.0250.06530.0085-0.01950.1116-0.10620.00450.0381-0.01360.00420.13970.01830.0337-15.1222-65.6018-16.4667
140.2817-0.02070.32970.02150.09531.1008-0.0729-0.2489-0.07090.06810.04110.0166-0.33660.07030.03780.41620.0079-0.09550.47010.14310.0968-5.0263-76.6507-7.4968
150.0563-0.05010.12191.0463-0.40480.37970.0012-0.0078-0.0334-0.021-0.0254-0.18240.06030.10550.01030.01350.0213-0.00810.0962-0.00650.0219-15.4774-50.8423-37.4067
160.006-0.0093-0.01230.35680.50160.7307-0.2937-0.1222-0.2309-0.03610.30720.14360.00480.3344-0.00690.17750.01210.09330.42820.15950.3078-5.8326-39.4461-46.447
170.28250.41850.34830.72780.3770.6413-0.0304-0.10290.00780.0928-0.01-0.0638-0.04160.12750.02340.0718-0.0264-0.00120.16160.01060.092815.1853-50.793539.9646
180.89090.3197-0.32160.1334-0.12290.1192-0.1053-0.50170.0042-0.0603-0.09360.00680.2619-0.09270.19530.2234-0.03440.07180.5668-0.10090.13795.1079-40.31449.6447
190.4374-0.2023-0.41280.28850.13350.82890.00730.0824-0.04220.0294-0.07380.03660.15990.13350.07060.01240.02250.0060.12130.03240.024315.5319-64.279718.2266
200.0406-0.0406-0.23920.09-0.02042.9341-0.05040.11-0.084-0.19910.0676-0.0255-0.4249-0.3345-0.00750.39410.0077-0.09110.6175-0.160.20896.078-75.13598.3793
210.48710.4645-0.46990.624-0.55330.8195-0.0216-0.1320.03160.0863-0.0432-0.0615-0.0622-0.07650.0160.0128-0.04260.04220.1009-0.00390.0482-15.087-65.713839.291
221.245-0.1241-0.08060.7693-0.91511.34310.1489-0.7047-0.3605-0.03580.04620.0980.0065-0.1387-0.18680.3746-0.1401-0.05890.6560.22150.4291-5.0935-76.712148.4164
230.391-0.46420.39840.8842-0.25041.0822-0.08340.0861-0.0012-0.02710.02850.1673-0.1467-0.25270.03180.0545-0.002800.13970.00620.0653-15.2499-50.781518.5463
240.127-0.00950.07810.00570.03591.26530.09570.06390.04-0.1263-0.1687-0.01820.60820.40610.07790.51760.03770.04020.50180.18390.2188-5.6066-39.3189.6094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND (RESSEQ 2:51 OR RESSEQ 58:142))
2X-RAY DIFFRACTION2(CHAIN A AND RESSEQ 52:57)
3X-RAY DIFFRACTION3(CHAIN B AND (RESSEQ 2:51 OR RESSEQ 58:142))
4X-RAY DIFFRACTION4(CHAIN B AND RESSEQ 52:57)
5X-RAY DIFFRACTION5(CHAIN C AND (RESSEQ 2:51 OR RESSEQ 58:142)
6X-RAY DIFFRACTION6(CHAIN C AND RESSEQ 52:57)
7X-RAY DIFFRACTION7(CHAIN D AND (RESSEQ 2:51 OR RESSEQ 58:142)
8X-RAY DIFFRACTION8(CHAIN D AND RESSEQ 52:57)
9X-RAY DIFFRACTION9(CHAIN E AND (RESSEQ 2:51 OR RESSEQ 58:142)
10X-RAY DIFFRACTION10(CHAIN E AND RESSEQ 52:57)
11X-RAY DIFFRACTION11(CHAIN F AND (RESSEQ 2:51 OR RESSEQ 58:142)
12X-RAY DIFFRACTION12(CHAIN F AND RESSEQ 52:57)
13X-RAY DIFFRACTION13(CHAIN G AND (RESSEQ 2:51 OR RESSEQ 58:142)
14X-RAY DIFFRACTION14(CHAIN G AND RESSEQ 52:57)
15X-RAY DIFFRACTION15(CHAIN H AND (RESSEQ 2:51 OR RESSEQ 58:142)
16X-RAY DIFFRACTION16(CHAIN H AND RESSEQ 52:57)
17X-RAY DIFFRACTION17(CHAIN I AND (RESSEQ 2:51 OR RESSEQ 58:142)
18X-RAY DIFFRACTION18(CHAIN I AND RESSEQ 52:57)
19X-RAY DIFFRACTION19(CHAIN J AND (RESSEQ 2:51 OR RESSEQ 58:142)
20X-RAY DIFFRACTION20(CHAIN J AND RESSEQ 52:57)
21X-RAY DIFFRACTION21(CHAIN K AND (RESSEQ 2:51 OR RESSEQ 58:142)
22X-RAY DIFFRACTION22(CHAIN K AND RESSEQ 52:57)
23X-RAY DIFFRACTION23(CHAIN L AND (RESSEQ 2:51 OR RESSEQ 58:142)
24X-RAY DIFFRACTION24(CHAIN L AND RESSEQ 52:57)

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  • 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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