[English] 日本語
Yorodumi
- PDB-5vnx: Crystal structure of an 8-amino-7-oxononanoate synthase from Burk... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vnx
TitleCrystal structure of an 8-amino-7-oxononanoate synthase from Burkholderia multivorans with a potential glycine-PLP-Lys242 cyclized intermediate or byproduct
Components8-amino-7-oxononanoate synthase
KeywordsTRANSFERASE / SSGCID / Burkholderia multivorans / 8-amino-7-oxononanoate synthase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


8-amino-7-oxononanoate synthase / 8-amino-7-oxononanoate synthase activity / biotin biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
8-amino-7-oxononanoate synthase, Proteobacteria / 8-amino-7-oxononanoate synthase, Archaea/Proteobacteria type / : / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...8-amino-7-oxononanoate synthase, Proteobacteria / 8-amino-7-oxononanoate synthase, Archaea/Proteobacteria type / : / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZAMIDINE / 8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a 8-amino-7-oxononanoate synthase from Burkholderia multivorans with a potential glycine-PLP-Lys242 cyclized intermediate or byproduct
Authors: Conrady, D.G. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMay 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.SG_entry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 8-amino-7-oxononanoate synthase
B: 8-amino-7-oxononanoate synthase
C: 8-amino-7-oxononanoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,78019
Polymers124,3943
Non-polymers1,38516
Water25,4551413
1
A: 8-amino-7-oxononanoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9877
Polymers41,4651
Non-polymers5236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 8-amino-7-oxononanoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8295
Polymers41,4651
Non-polymers3644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 8-amino-7-oxononanoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9637
Polymers41,4651
Non-polymers4986
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)177.530, 262.090, 65.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-922-

HOH

21B-887-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 12 or resid 14...
21(chain B and ((resid 2 and (name N or name...
31(chain C and ((resid 2 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNALAALA(chain A and (resid 2 through 12 or resid 14...AA2 - 122 - 12
12LEULEULEULEU(chain A and (resid 2 through 12 or resid 14...AA1414
13ALAALAALAALA(chain A and (resid 2 through 12 or resid 14...AA16 - 2616 - 26
14SERSERHISHIS(chain A and (resid 2 through 12 or resid 14...AA28 - 3328 - 33
15THRTHRGLYGLY(chain A and (resid 2 through 12 or resid 14...AA35 - 3835 - 38
16ARGARGARGARG(chain A and (resid 2 through 12 or resid 14...AA3939
17METMETALAALA(chain A and (resid 2 through 12 or resid 14...AA1 - 3931 - 393
18METMETALAALA(chain A and (resid 2 through 12 or resid 14...AA1 - 3931 - 393
19METMETALAALA(chain A and (resid 2 through 12 or resid 14...AA1 - 3931 - 393
110METMETALAALA(chain A and (resid 2 through 12 or resid 14...AA1 - 3931 - 393
21ASNASNASNASN(chain B and ((resid 2 and (name N or name...BB22
22ASNASNALAALA(chain B and ((resid 2 and (name N or name...BB2 - 3932 - 393
23ASNASNALAALA(chain B and ((resid 2 and (name N or name...BB2 - 3932 - 393
24ASNASNALAALA(chain B and ((resid 2 and (name N or name...BB2 - 3932 - 393
25ASNASNALAALA(chain B and ((resid 2 and (name N or name...BB2 - 3932 - 393
31ASNASNASNASN(chain C and ((resid 2 and (name N or name...CC22
32ASNASNALAALA(chain C and ((resid 2 and (name N or name...CC2 - 3932 - 393
33ASNASNALAALA(chain C and ((resid 2 and (name N or name...CC2 - 3932 - 393
34ASNASNALAALA(chain C and ((resid 2 and (name N or name...CC2 - 3932 - 393
35ASNASNALAALA(chain C and ((resid 2 and (name N or name...CC2 - 3932 - 393

-
Components

#1: Protein 8-amino-7-oxononanoate synthase / AONS / 7-keto-8-amino-pelargonic acid synthase / KAPA synthase / 8-amino-7-ketopelargonate synthase


Mass: 41464.793 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria)
Strain: ATCC 17616 / 249 / Gene: bioF, Bmul_0373, BMULJ_02881 / Plasmid: BumuA.00096.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A9AE46, 8-amino-7-oxononanoate synthase
#2: Chemical
ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1413 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: BumuA.00096.a.B1.PW37876 at 21.8mg/ml, mixed 1:1 with MCSG1 F10:, 0.1M Tris HCl pH 8.5, 2M Ammonium Sulfate, cryo protected with 25% EG

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→44.383 Å / Num. obs: 182627 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.494 % / Biso Wilson estimate: 18.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.071 / Χ2: 0.98 / Net I/σ(I): 18.8 / Num. measured all: 1368551 / Scaling rejects: 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.697.4720.5563.6210024913418134160.8970.598100
1.69-1.747.4830.4494.459762013047130460.9310.482100
1.74-1.797.4960.3615.519506612683126820.950.388100
1.79-1.847.5070.2787.079267012345123450.9720.299100
1.84-1.917.5160.2248.649007411985119850.9810.241100
1.91-1.977.530.17610.938756511629116290.9870.189100
1.97-2.057.5310.13513.778410211167111670.9920.145100
2.05-2.137.5370.11116.38087610731107310.9940.119100
2.13-2.227.540.09219.47838010395103950.9950.099100
2.22-2.337.5360.07922.1174777992299220.9970.085100
2.33-2.467.5390.07124.4270662937393730.9970.077100
2.46-2.617.5410.06526.2367476894989480.9970.07100
2.61-2.797.5360.05829.5763256839483940.9970.062100
2.79-3.017.5250.05332.159218787078690.9980.057100
3.01-3.37.5020.04836.0754353724572450.9980.051100
3.3-3.697.4710.04439.2148992655965580.9980.047100
3.69-4.267.4370.04241.5343385583658340.9980.045100
4.26-5.227.3730.04142.1136497495049500.9980.044100
5.22-7.387.2630.0441.3328390391039090.9980.044100
7.38-44.3836.7040.04141.9214943225722290.9970.04598.8

-
Processing

Software
NameVersionClassification
PHENIXdev_2733refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5jay

5jay


Resolution: 1.65→44.383 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1673 2011 1.1 %
Rwork0.1456 180604 -
obs0.1459 182615 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.42 Å2 / Biso mean: 23.5045 Å2 / Biso min: 9.28 Å2
Refinement stepCycle: final / Resolution: 1.65→44.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8646 0 92 1445 10183
Biso mean--49.6 35.56 -
Num. residues----1177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119436
X-RAY DIFFRACTIONf_angle_d1.36512939
X-RAY DIFFRACTIONf_chiral_restr0.081508
X-RAY DIFFRACTIONf_plane_restr0.0081700
X-RAY DIFFRACTIONf_dihedral_angle_d14.0225632
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4378X-RAY DIFFRACTION2.486TORSIONAL
12B4378X-RAY DIFFRACTION2.486TORSIONAL
13C4378X-RAY DIFFRACTION2.486TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.65-1.69130.2241520.18571276912921
1.6913-1.7370.20021370.17811282412961
1.737-1.78810.19481440.17251277812922
1.7881-1.84580.20371400.16371276512905
1.8458-1.91180.20131520.15871283512987
1.9118-1.98830.15621260.15061285412980
1.9883-2.07880.17461380.14831281112949
2.0788-2.18840.18721460.14471284512991
2.1884-2.32550.17251510.14071285913010
2.3255-2.50510.1581420.14551291013052
2.5051-2.75710.16651340.1471292813062
2.7571-3.1560.17621570.15091295613113
3.156-3.97590.14451570.13041302713184
3.9759-44.39850.151350.13771344313578
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.03260.4806-0.13213.7028-0.86231.9812-0.03370.01020.132-0.178-0.0098-0.0757-0.20890.43720.08380.1591-0.0621-0.01080.292-0.01530.159375.840354.027214.9878
21.04940.00650.3050.64940.60732.2097-0.0190.1195-0.1446-0.05290.0016-0.00270.25150.13780.00080.1570.02340.00550.09090.01730.132258.37330.418815.7847
30.2172-0.0699-0.03021.10590.1511.28140.00430.01710.0451-0.06670.00370.0647-0.0604-0.0344-0.00690.1127-0.008-0.00440.10790.01490.138847.097647.967525.481
40.5663-0.01770.11390.6984-0.03010.8989-0.0164-0.04910.04960.0790.0129-0.129-0.03890.2769-0.00070.11690.0008-0.00970.20810.00520.135570.035947.026430.5181
52.3731-0.633-1.47971.20641.37034.1372-0.00910.00890.0699-0.0674-0.11930.28310.2156-0.56070.13640.1865-0.0398-0.03860.25210.0030.231439.519432.75677.1869
60.89860.92021.36081.26170.92873.15380.1599-0.0006-0.11340.0008-0.0141-0.15010.41130.3528-0.14810.17780.06080.02580.17390.00480.136265.357529.79912.9619
70.2591-0.11090.36910.3331-0.22283.31530.0037-0.0314-0.02860.03220.0296-0.09090.0560.4745-0.04170.09870.00680.0010.22570.00390.160572.553143.69349.2376
82.2315-1.15990.6711.0098-0.53651.7353-0.1091-0.18230.06750.08760.1204-0.0288-0.27540.118-0.02710.1429-0.0243-0.01740.1455-0.02060.108461.308555.31412.3666
92.2473-1.18310.4551.7846-0.10692.4533-0.0819-0.13250.10050.13160.04750.0684-0.2783-0.04020.02770.17360.0061-0.00380.10020.00310.127350.67860.7668-3.2424
103.50021.6986-0.30095.50960.33732.5199-0.0160.17960.135-0.25270.0440.0516-0.14120.0329-0.03820.11380.021-0.01650.11780.01240.087355.315455.1922-12.3433
111.6033-0.9653-0.22363.116801.7949-0.01410.0036-0.01040.0159-0.006-0.0640.00660.18270.01770.1041-0.011-0.00090.1368-0.00670.087962.581747.9329-8.8863
121.09140.2710.36892.4335-0.11762.8626-0.0033-0.07320.07680.0919-0.0183-0.0424-0.11460.18580.03340.0846-0.00510.00010.1462-0.00450.108465.398351.33640.0509
130.65460.31541.3930.7344-0.04013.8155-0.0229-0.124-0.03260.0790.1262-0.08750.23040.3592-0.1440.0782-0.01430.00890.180.01860.150967.105341.15336.7898
144.0694-0.03471.21731.461-0.08612.09290.01490.133-0.0698-0.30050.02060.01790.25740.0678-0.05310.22290.0148-0.00520.1001-0.02070.093254.574831.5048-17.7008
152.62820.6363-1.83622.0119-1.51792.92760.04710.09060.1509-0.16560.09170.39150.1133-0.3455-0.13440.1844-0.0356-0.06080.1781-0.02240.18738.627234.6408-10.8713
162.9479-1.0492-0.62561.4176-0.12681.58930.03560.0357-0.0892-0.1650.02550.1960.1145-0.1682-0.04570.2094-0.0336-0.05130.11110.00270.133542.044931.0677-10.0119
171.47680.8130.58293.5967-0.21941.8046-0.00230.137-0.0257-0.50030.11550.19770.1888-0.2746-0.06510.2809-0.0321-0.00830.22310.02980.180726.08012.553411.3764
180.3544-0.0517-0.39741.4888-0.4571.0518-0.0678-0.071-0.01760.0916-0.0261-0.18670.02140.15190.10560.1017-0.0221-0.0370.15660.02360.180737.17695.346938.4934
192.8122-0.97870.93911.5385-0.63220.5843-0.0287-0.0715-0.31540.1080.1120.37150.0075-0.0916-0.07320.15170.00150.01920.13540.0230.240312.122112.059838.1125
202.72460.8316-2.83662.5208-0.04348.7175-0.03660.07250.1986-0.00220.09620.1267-0.3714-0.1043-0.08550.1120.0182-0.0450.08730.01250.193515.105423.440835.3193
211.3922-0.82750.07141.6281-0.26180.747-0.0575-0.0861-0.04390.15110.01220.0878-0.04790.0270.04140.1353-0.0207-0.01340.11360.00430.12226.341111.951340.5436
222.14270.73570.45882.05880.11091.9145-0.05880.28130.1373-0.2585-0.0330.1455-0.0115-0.09540.09520.1882-0.0326-0.02040.16550.04260.182227.980221.846813.7722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 42 )A1 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 97 )A43 - 97
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 264 )A98 - 264
4X-RAY DIFFRACTION4chain 'A' and (resid 265 through 393 )A265 - 393
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 42 )B2 - 42
6X-RAY DIFFRACTION6chain 'B' and (resid 43 through 69 )B43 - 69
7X-RAY DIFFRACTION7chain 'B' and (resid 70 through 97 )B70 - 97
8X-RAY DIFFRACTION8chain 'B' and (resid 98 through 133 )B98 - 133
9X-RAY DIFFRACTION9chain 'B' and (resid 134 through 179 )B134 - 179
10X-RAY DIFFRACTION10chain 'B' and (resid 180 through 201 )B180 - 201
11X-RAY DIFFRACTION11chain 'B' and (resid 202 through 227 )B202 - 227
12X-RAY DIFFRACTION12chain 'B' and (resid 228 through 264 )B228 - 264
13X-RAY DIFFRACTION13chain 'B' and (resid 265 through 291 )B265 - 291
14X-RAY DIFFRACTION14chain 'B' and (resid 292 through 314 )B292 - 314
15X-RAY DIFFRACTION15chain 'B' and (resid 315 through 347 )B315 - 347
16X-RAY DIFFRACTION16chain 'B' and (resid 348 through 393 )B348 - 393
17X-RAY DIFFRACTION17chain 'C' and (resid 2 through 42 )C2 - 42
18X-RAY DIFFRACTION18chain 'C' and (resid 43 through 97 )C43 - 97
19X-RAY DIFFRACTION19chain 'C' and (resid 98 through 179 )C98 - 179
20X-RAY DIFFRACTION20chain 'C' and (resid 180 through 201 )C180 - 201
21X-RAY DIFFRACTION21chain 'C' and (resid 202 through 291 )C202 - 291
22X-RAY DIFFRACTION22chain 'C' and (resid 292 through 393 )C292 - 393

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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

-
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

Read more