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- PDB-2bwj: Structure of adenylate kinase 5 -

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Basic information

Entry
Database: PDB / ID: 2bwj
TitleStructure of adenylate kinase 5
ComponentsADENYLATE KINASE 5
KeywordsTRANSFERASE / ADENYLATE KINASE / PHOSPHORYL TRANSFER REACTION
Function / homology
Function and homology information


dADP biosynthetic process / : / purine nucleotide metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / pyrimidine ribonucleotide biosynthetic process / adenylate kinase activity / nucleobase-containing small molecule interconversion / nucleoside-diphosphate kinase ...dADP biosynthetic process / : / purine nucleotide metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / pyrimidine ribonucleotide biosynthetic process / adenylate kinase activity / nucleobase-containing small molecule interconversion / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / nucleoside diphosphate kinase activity / centriolar satellite / ATP metabolic process / ATP binding / cytoplasm / cytosol
Similarity search - Function
Adenylate kinase, isozyme 1/5 / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Adenylate kinase isoenzyme 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsBunkoczi, G. / Filippakopoulos, P. / Fedorov, O. / Jansson, A. / Longman, E. / Ugochukwu, E. / Knapp, S. / von Delft, F. / Arrowsmith, C. / Edwards, A. ...Bunkoczi, G. / Filippakopoulos, P. / Fedorov, O. / Jansson, A. / Longman, E. / Ugochukwu, E. / Knapp, S. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J.
CitationJournal: To be Published
Title: Structure of Adenylate Kinase 5
Authors: Filippakopoulos, P. / Bunkoczi, G. / Jansson, A. / Longman, E. / Knapp, S.
History
DepositionJul 14, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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: ADENYLATE KINASE 5
B: ADENYLATE KINASE 5
C: ADENYLATE KINASE 5
D: ADENYLATE KINASE 5
E: ADENYLATE KINASE 5
F: ADENYLATE KINASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,95121
Polymers133,0596
Non-polymers1,89115
Water8,287460
1
A: ADENYLATE KINASE 5
B: ADENYLATE KINASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0598
Polymers44,3532
Non-polymers7066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: ADENYLATE KINASE 5
F: ADENYLATE KINASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3118
Polymers44,3532
Non-polymers9576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
D: ADENYLATE KINASE 5
E: ADENYLATE KINASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5815
Polymers44,3532
Non-polymers2283
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)180.375, 180.375, 121.701
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51F
12A
22B
32C
42D
52E
62F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A3 - 11
2115B3 - 11
3115C3 - 11
4115D3 - 11
5115F3 - 11
1125A11 - 198
2125B11 - 198
3125C11 - 198
4125D11 - 198
5125E11 - 198
6125F11 - 198

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.41984, -0.90519, 0.06603), (-0.90563, 0.41303, -0.09609), (0.05971, -0.10014, -0.99318)147.22264, 93.15382, -2.42559
2given(-0.57113, -0.24643, 0.78299), (0.23157, 0.86676, 0.44171), (-0.78752, 0.43359, -0.43797)148.4165, 17.35153, 81.46748
3given(0.36442, -0.91428, 0.1769), (-0.16426, -0.2501, -0.95418), (0.91663, 0.31866, -0.24132)106.4955, 17.93164, -74.65356
4given(0.60795, -0.79353, -0.02653), (0.21803, 0.13472, 0.9666), (-0.76346, -0.59343, 0.25491)81.50393, -25.39286, 97.05065
5given(0.56054, 0.27703, -0.78041), (-0.82652, 0.1285, -0.54804), (-0.05154, 0.95223, 0.301)34.93513, 128.80684, 4.32571

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Components

#1: Protein
ADENYLATE KINASE 5 / ATP-AMP / TRANSPHOSPHORYLASE5


Mass: 22176.564 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC-SGC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y6K8, adenylate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 135 TO MET ENGINEERED RESIDUE IN CHAIN B, ARG 135 TO MET ...ENGINEERED RESIDUE IN CHAIN A, ARG 135 TO MET ENGINEERED RESIDUE IN CHAIN B, ARG 135 TO MET ENGINEERED RESIDUE IN CHAIN C, ARG 135 TO MET ENGINEERED RESIDUE IN CHAIN D, ARG 135 TO MET ENGINEERED RESIDUE IN CHAIN E, ARG 135 TO MET ENGINEERED RESIDUE IN CHAIN F, ARG 135 TO MET
Sequence detailsRESIDUE 1 REMAINS FROM HIS-TAG AFTER TEV CLEAVAGE

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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: 4.2 Å3/Da / Density % sol: 70.7 % / Description: NCS AVERAGING DONE WITH DM.
Crystal growpH: 7.5
Details: 0.1M HEPES PH7.5, 0.1M NACL, 1.6M (NH4)2SO4, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 13, 2005 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→48.15 Å / Num. obs: 7913 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.53
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.35 / % possible all: 63.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 9.839 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 4454 5 %RANDOM
Rwork0.172 ---
obs0.174 84202 88.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20.79 Å20 Å2
2--1.58 Å20 Å2
3----2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8699 0 101 460 9260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228947
X-RAY DIFFRACTIONr_bond_other_d0.0010.028349
X-RAY DIFFRACTIONr_angle_refined_deg1.3482.00612118
X-RAY DIFFRACTIONr_angle_other_deg0.776319333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.20751166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.924.344343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.562151571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9861556
X-RAY DIFFRACTIONr_chiral_restr0.070.21428
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021701
X-RAY DIFFRACTIONr_nbd_refined0.1950.21981
X-RAY DIFFRACTIONr_nbd_other0.1670.28151
X-RAY DIFFRACTIONr_nbtor_refined0.1730.24437
X-RAY DIFFRACTIONr_nbtor_other0.0860.25364
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2465
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.94735918
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.15659260
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.45683376
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it11.69112851
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
11A41medium positional0.320.5
12B41medium positional0.260.5
13C41medium positional0.190.5
14D41medium positional0.220.5
15F41medium positional0.310.5
21A1083medium positional0.380.5
22B1083medium positional0.670.5
23C1083medium positional0.330.5
24D1083medium positional0.30.5
25E1083medium positional0.420.5
26F1083medium positional0.410.5
11A22loose positional0.615
12B22loose positional0.545
13C22loose positional0.685
14D22loose positional0.75
15F22loose positional0.765
21A1390loose positional0.785
22B1390loose positional1.095
23C1390loose positional0.695
24D1390loose positional0.895
25E1390loose positional0.945
26F1390loose positional0.745
11A41medium thermal1.42
12B41medium thermal0.762
13C41medium thermal0.772
14D41medium thermal0.362
15F41medium thermal0.82
21A1083medium thermal1.162
22B1083medium thermal1.152
23C1083medium thermal0.922
24D1083medium thermal0.642
25E1083medium thermal0.852
26F1083medium thermal0.972
11A22loose thermal3.1210
12B22loose thermal1.2910
13C22loose thermal1.710
14D22loose thermal1.5110
15F22loose thermal1.7810
21A1390loose thermal3.1910
22B1390loose thermal3.3710
23C1390loose thermal2.7510
24D1390loose thermal3.1610
25E1390loose thermal2.7510
26F1390loose thermal2.8610
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.287 191
Rwork0.212 3381
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)
14.09251.9185-0.90024.6562-2.06842.761-0.28050.1237-0.1498-0.32230.12860.14950.5003-0.16590.1519-0.0056-0.12610.0168-0.2318-0.0102-0.415185.21033.49519.4133
21.5424-0.2022-1.2531.6874-1.78134.8891-0.08180.1785-0.0508-0.42270.0424-0.0690.7411-0.24010.03940.0976-0.1571-0.0175-0.2118-0.0093-0.358488.37553.30773.7512
30.9709-0.15540.1636.22760.13274.6737-0.43060.09230.3079-0.89620.2736-0.0784-0.0176-0.28660.157-0.0214-0.1773-0.0673-0.14560.0388-0.265681.42929.284612.5155
43.72440.4957-0.28781.6335-0.35740.94380.0495-0.1370.0817-0.0113-0.06180.0039-0.0377-0.02690.0122-0.0978-0.0565-0.0514-0.32190.0019-0.403197.726717.26518.907
55.15370.98650.23662.2617-0.32352.1830.2017-0.47120.04950.2993-0.20730.11850.0617-0.03770.0056-0.064-0.09070.0034-0.22050.0193-0.391288.19537.860730.6773
69.72091.84091.72772.91990.9646.1919-0.28270.27790.5497-0.08010.1863-0.4916-0.68140.75330.09630.0365-0.136-0.0118-0.10620.0143-0.3308109.106614.7966-17.6554
72.0099-0.0068-1.50462.43740.30157.2146-0.19470.0551-0.06430.04940.1486-0.06050.2910.60380.0461-0.1233-0.0722-0.0551-0.2496-0.0142-0.3114107.571214.3896-0.9282
86.4725-0.459-1.78653.72221.67278.86-0.0606-0.14850.4667-0.14050.241-0.0693-0.79750.3303-0.18030.0063-0.1734-0.0271-0.21850.0254-0.332105.720222.2459-10.506
92.67461.8757-0.71335.6232-0.36444.12380.00430.08070.03570.1842-0.03960.26610.0084-0.46530.0353-0.0566-0.0588-0.0092-0.16210.0065-0.373291.92579.9842-17.4915
102.9246-0.43061.58325.6244.33516.81250.00060.4840.3955-0.65860.2364-0.332-0.71480.6085-0.2370.0767-0.19050.0569-0.16790.0225-0.3291104.628813.5056-28.3399
114.20790.12870.04727.3867-1.44184.68690.02310.1962-0.49420.2401-0.383-1.35130.40230.7730.3599-0.2122-0.0573-0.10720.09910.0830.1165113.513550.16545.7211
123.02691.2608-0.88864.9841-1.33154.4544-0.3964-0.0452-0.3370.0309-0.0151-0.40640.28050.27310.4115-0.11860.0307-0.1154-0.2172-0.0385-0.189499.978342.298211.688
135.6556-1.488-2.50655.8365-0.17067.4299-0.1922-0.3994-0.31080.5652-0.1645-0.7425-0.33120.67170.3567-0.1174-0.0804-0.2439-0.05280.0594-0.0393108.86449.947616.3234
144.5224-0.61052.83251.6519-0.91145.18070.0021-0.03070.12410.2473-0.073-0.3863-0.35260.27020.0709-0.1199-0.074-0.1132-0.14350.0183-0.1702102.984963.28483.4752
157.93590.1725-0.55587.73090.89033.5297-0.13790.4533-0.10360.0303-0.3918-1.5662-0.04421.19130.5297-0.1704-0.154-0.04360.33630.15570.3862119.699858.72671.6787
162.9387-0.42943.56973.0199-2.6217.43680.02851.3015-0.0944-1.61080.252-0.64431.0170.7312-0.28051.09410.1360.05550.2502-0.03650.4917137.8651-17.00562.3528
175.9935-3.5260.050713.13773.08156.82380.42770.05410.0707-1.1573-0.0078-1.08280.6968-0.0086-0.41990.3327-0.0207-0.06130.09090.15930.2775135.9537-0.39676.7678
184.2292-0.05551.16678.9841.55570.5966-0.43990.29530.9735-2.08650.36210.30141.7922-0.22090.07781.0643-0.1012-0.28140.46590.07920.4148130.0518-9.72190.3464
194.349-0.22452.44984.5543-3.60612.264-0.02720.2967-0.2177-0.85890.28620.31020.7877-0.7238-0.2590.50170.0287-0.1828-0.16420.0950.4432129.9095-20.494116.4893
206.43321.7025-5.28265.8166-3.51257.9530.43220.674-0.5827-1.25460.53390.04752.09090.3245-0.96611.34650.2126-0.06680.1309-0.11670.653136.966-28.52962.8423
214.8303-0.53081.12885.1145-0.99215.7643-0.0884-0.9310.13780.9757-0.0093-0.6098-0.46960.53450.09770.0628-0.0673-0.2761-0.0432-0.00980.0902131.146414.954132.3223
223.0286-0.1947-0.34311.43922.17442.5396-0.2127-0.2368-0.28460.49650.2072-0.3720.66530.35580.00560.09260.0807-0.2036-0.07860.17890.1593132.2819-2.19728.5923
2311.0195-0.00733.4164.8861-0.15795.51050.0426-0.1559-0.65630.84230.2541-0.09260.58090.2019-0.29670.1376-0.001-0.1601-0.06790.1146-0.0259123.08785.264932.5229
245.54720.7008-0.92023.4875-0.72566.0429-0.20840.10690.0648-0.07540.0269-0.7438-0.12520.23970.1815-0.1491-0.0449-0.0752-0.28360.0663-0.0108126.710816.607117.0654
256.95581.91911.28825.2879-2.16568.0757-0.1759-0.71610.81031.0379-0.036-0.709-1.04420.15310.21190.3462-0.0185-0.2703-0.0945-0.13720.1559128.487324.992932.4118
267.1542-1.85372.32165.7859-1.31145.1637-0.11120.45220.4448-0.33020.0280.6223-0.2439-0.94560.0833-0.1845-0.0057-0.07830.1160.0145-0.150968.691146.472410.0677
275.31712.2985-1.29842.9542-0.16842.4491-0.17510.47740.408-0.21290.2810.2432-0.0383-0.3606-0.1059-0.13370.0534-0.1146-0.09720.0211-0.252582.785354.30013.7947
281.9817-0.3899-3.16263.46120.73665.66050.12170.34740.66970.03690.12790.449-0.2995-0.3297-0.2497-0.16490.12-0.0875-0.04230.0454-0.07473.329155.440412.5224
291.907-1.85250.23733.73650.07491.7298-0.0441-0.09750.04460.14350.08680.197-0.0802-0.3148-0.0427-0.1451-0.0268-0.0124-0.1836-0.0281-0.289779.578739.943421.5663
302.92480.18481.57853.029-0.18846.5829-0.02010.0253-0.3264-0.13950.321.10140.352-1.6004-0.2999-0.2029-0.1375-0.02710.2932-0.00030.097962.768239.358116.7969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 34
2X-RAY DIFFRACTION2A35 - 89
3X-RAY DIFFRACTION3A90 - 113
4X-RAY DIFFRACTION4A114 - 171
5X-RAY DIFFRACTION5A172 - 198
6X-RAY DIFFRACTION6B4 - 34
7X-RAY DIFFRACTION7B35 - 89
8X-RAY DIFFRACTION8B90 - 113
9X-RAY DIFFRACTION9B114 - 171
10X-RAY DIFFRACTION10B172 - 198
11X-RAY DIFFRACTION11C5 - 34
12X-RAY DIFFRACTION12C35 - 89
13X-RAY DIFFRACTION13C90 - 113
14X-RAY DIFFRACTION14C114 - 171
15X-RAY DIFFRACTION15C172 - 197
16X-RAY DIFFRACTION16D5 - 34
17X-RAY DIFFRACTION17D35 - 89
18X-RAY DIFFRACTION18D90 - 113
19X-RAY DIFFRACTION19D114 - 171
20X-RAY DIFFRACTION20D172 - 196
21X-RAY DIFFRACTION21E8 - 34
22X-RAY DIFFRACTION22E35 - 89
23X-RAY DIFFRACTION23E90 - 113
24X-RAY DIFFRACTION24E114 - 171
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26X-RAY DIFFRACTION26F5 - 34
27X-RAY DIFFRACTION27F35 - 89
28X-RAY DIFFRACTION28F90 - 113
29X-RAY DIFFRACTION29F114 - 171
30X-RAY DIFFRACTION30F172 - 198

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