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- PDB-3u0g: Crystal structure of branched-chain amino acid aminotransferase f... -

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Basic information

Entry
Database: PDB / ID: 3u0g
TitleCrystal structure of branched-chain amino acid aminotransferase from burkholderia pseudomallei
ComponentsPutative branched-chain amino acid aminotransferase IlvE
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / PyridoxaL 5'-Phosphate Dependent Enzymes class IV / branched chain amino transferase / PyridoxaL 5'-Phosphate
Function / homology
Function and homology information


branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process
Similarity search - Function
Branched-chain amino acid aminotransferase I / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal ...Branched-chain amino acid aminotransferase I / Branched-chain aminotransferase / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Branched-chain-amino-acid aminotransferase / Branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of branched-chain amino acid aminotransferase from burkholderia pseudomallei
Authors: Staker, B.L. / Gardberg, A. / Sankaran, B. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionSep 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative branched-chain amino acid aminotransferase IlvE
B: Putative branched-chain amino acid aminotransferase IlvE
C: Putative branched-chain amino acid aminotransferase IlvE
D: Putative branched-chain amino acid aminotransferase IlvE
E: Putative branched-chain amino acid aminotransferase IlvE
F: Putative branched-chain amino acid aminotransferase IlvE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,98521
Polymers217,9276
Non-polymers1,05915
Water12,106672
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29730 Å2
ΔGint-231 kcal/mol
Surface area56250 Å2
MethodPISA
2
A: Putative branched-chain amino acid aminotransferase IlvE
B: Putative branched-chain amino acid aminotransferase IlvE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9036
Polymers72,6422
Non-polymers2614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-78 kcal/mol
Surface area22700 Å2
MethodPISA
3
C: Putative branched-chain amino acid aminotransferase IlvE
D: Putative branched-chain amino acid aminotransferase IlvE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9957
Polymers72,6422
Non-polymers3535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-82 kcal/mol
Surface area22460 Å2
MethodPISA
4
E: Putative branched-chain amino acid aminotransferase IlvE
F: Putative branched-chain amino acid aminotransferase IlvE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0878
Polymers72,6422
Non-polymers4456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-80 kcal/mol
Surface area22940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.970, 139.270, 290.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-332-

HOH

21A-602-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
12B
13C
14D
15E
16F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A0 - 999
1125B0 - 999
1135C0 - 999
1145D0 - 999
1155E0 - 999
1165F0 - 999

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Putative branched-chain amino acid aminotransferase IlvE


Mass: 36321.105 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710B / Gene: ilvE, BPSL0793 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q63WU8, UniProt: Q3JVJ9*PLUS, branched-chain-amino-acid transaminase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 20% PEG 8000, 100MM CHES, PROTEIN CONCENTRATION 23.1 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 9.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97651
ReflectionResolution: 1.9→20 Å / Num. obs: 126128 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.076

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WRV
Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.373 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22964 8508 5 %RANDOM
Rwork0.19173 ---
obs0.1936 126128 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.994 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--3.6 Å20 Å2
3----3.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13866 0 54 672 14592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01914234
X-RAY DIFFRACTIONr_bond_other_d0.0010.029459
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.93719296
X-RAY DIFFRACTIONr_angle_other_deg0.999322918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5651793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66323.437643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.509152333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.72215108
X-RAY DIFFRACTIONr_chiral_restr0.0990.22166
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216018
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023070
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1692medium positional0.160.5
2B1692medium positional0.160.5
3C1692medium positional0.190.5
4D1692medium positional0.170.5
5E1692medium positional0.190.5
6F1692medium positional0.220.5
1A1946loose positional0.345
2B1946loose positional0.325
3C1946loose positional0.325
4D1946loose positional0.375
5E1946loose positional0.375
6F1946loose positional0.375
1A1692medium thermal2.22
2B1692medium thermal2.772
3C1692medium thermal2.972
4D1692medium thermal3.242
5E1692medium thermal3.62
6F1692medium thermal4.962
1A1946loose thermal2.5310
2B1946loose thermal2.8810
3C1946loose thermal3.0610
4D1946loose thermal3.3710
5E1946loose thermal3.810
6F1946loose thermal5.5610
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 604 -
Rwork0.32 11336 -
obs--99.79 %
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)
13.10410.2729-0.69742.01351.44757.3640.1542-0.0311-0.2465-0.1062-0.15810.00220.279-0.17840.00380.0478-0.0069-0.04750.35680.00360.16992.626410.465280.0197
21.51260.25710.34271.4611-0.07221.98930.1115-0.1033-0.16850.0223-0.04140.12110.2331-0.6036-0.07010.0339-0.0638-0.01660.27920.01390.13566.060910.06293.2852
32.97071.59420.11045.42710.45153.79740.12310.0172-0.00090.04610.0379-0.2965-0.044-0.398-0.16110.0130.0119-0.02510.2760.00840.134810.306715.753688.153
40.7494-0.58310.1470.4627-0.0321.53840.07860.0391-0.1363-0.0284-0.04740.0870.3193-0.2998-0.03120.163-0.0612-0.02140.09220.01590.197628.11235.379596.3614
55.01240.5951-1.52092.1133-1.00561.81760.1327-0.34750.10860.06220.0182-0.08790.3479-0.2334-0.15090.2268-0.1546-0.04950.13040.03390.23521.4665-1.8587108.3632
63.58570.2410.38820.2655-0.41192.12590.1564-0.0512-0.3838-0.0343-0.00920.06360.5984-0.3135-0.14720.3278-0.165-0.04120.09590.02880.291720.5784-7.9879103.8232
76.3231-0.7854-1.12223.1754-1.06074.0869-0.07280.37160.1872-0.07470.00740.3141-0.3456-0.4780.06530.08140.1016-0.04550.29490.05350.114212.906227.748671.9525
81.601-0.21270.60921.1943-0.36012.014-0.00660.33960.1942-0.0694-0.1221-0.0554-0.31150.07670.12870.10070.0193-0.01550.15630.05020.117826.263428.011476.5563
91.14870.29690.83692.82930.76452.68380.05560.1401-0.0499-0.0342-0.09880.21560.0304-0.21480.04320.01250.03550.01270.2110.03230.133420.515221.00581.3886
100.4626-0.24120.15020.23690.36222.5485-0.01370.11570.0701-0.03-0.0762-0.025-0.3536-0.21380.08990.1826-0.0051-0.01630.10670.02530.189427.575128.420499.2793
110.7803-0.4585-0.19852.1481-0.4015.5803-0.1220.18860.20940.0648-0.1586-0.0538-0.34490.58350.28060.243-0.1417-0.07480.15880.12610.23541.2938.340993.3487
121.6187-0.40090.1380.7966-0.87645.0506-0.13740.21660.32940.1082-0.0425-0.1324-0.88620.1120.17990.4024-0.1332-0.07460.07290.07330.290335.463743.669293.6579
136.94240.8951-0.51235.0678-2.58981.37390.0743-0.6398-0.1226-0.3638-0.5004-0.76520.36750.39070.42610.70640.48660.0930.4990.15150.498364.8895-20.4635115.8456
141.03050.2985-0.30661.2256-0.3532.5445-0.0081-0.0145-0.2397-0.0298-0.0117-0.08510.70630.35620.01990.30660.17270.00720.12080.04320.161651.9007-16.2236114.9298
151.8810.9125-1.03822.53050.08334.7596-0.10510.1546-0.0914-0.28650.0422-0.21610.55070.75640.06290.19820.18510.02560.25230.01380.258457.6229-11.6571109.0822
161.42740.09530.34220.49140.36812.5149-0.0437-0.0237-0.09660.11140.03110.00380.2220.52510.01270.12590.0197-0.00310.13440.04140.124548.59355.6436120.6896
170.67180.25450.79224.1592-1.17193.91150.0553-0.01430.083-0.19750.08950.35030.08760.0599-0.14490.1698-0.01730.01790.0630.07670.157335.4656-1.6451126.2182
180.1320.43470.14933.1992-0.46060.94820.0211-0.01760.0060.1660.02860.08710.16990.0146-0.04970.22610.01120.02530.11130.04320.125839.2923-3.121132.7475
190.53230.3128-0.95270.894-0.69463.4234-0.14370.0181-0.254-0.1069-0.0246-0.29810.31090.58480.16830.16710.14870.06730.62670.0220.277671.8847-1.5347100.4057
200.93060.4721-0.68511.50220.9174.3912-0.0888-0.1204-0.2292-0.19660.1069-0.2919-0.04190.8247-0.01820.04060.06650.03620.59730.02890.157173.28145.6863103.8257
211.6473-0.55340.10172.1286-0.0050.02040.08920.079-0.18990.111-0.0713-0.24660.06150.0479-0.0180.23380.1460.03120.67990.04860.319366.3671-0.0657105.2368
220.8674-0.07070.17050.8011-0.17272.16740.04950.161-0.0384-0.0232-0.0701-0.0640.20490.47920.02060.05070.03570.00840.18770.01580.099549.25567.730697.3513
238.0293-0.0125-1.41770.00060.00934.58610.3174-0.59530.59920.0039-0.00760.0065-0.30640.2181-0.30980.2099-0.10730.11110.34470.00580.214257.223922.227291.2976
244.45050.2256-0.99250.16830.08730.54810.12720.2060.138-0.07-0.0059-0.0194-0.12640.2197-0.12130.1542-0.02190.03320.44630.01150.140757.036316.893785.0909
251.00720.54170.01930.9445-1.11884.2824-0.1729-0.17620.1760.45230.08050.0168-1.4498-0.93890.09240.64640.2563-0.02480.3775-0.05910.142228.298834.3784143.1757
262.863-0.35030.57370.86710.13325.8069-0.173-0.3580.0430.2077-0.03690.0703-0.6767-0.76760.20990.27310.08710.00460.2336-0.03430.085629.95626.2733144.6089
270.75361.30760.92142.49331.1316.8871-0.135-0.10450.13440.2448-0.27960.0802-1.5126-0.73320.41460.76980.1577-0.16790.38810.01110.219930.416232.6978138.1994
281.1764-0.43041.18980.7916-0.08712.6456-0.1086-0.210.09210.1726-0.01420.0216-0.3235-0.56690.12270.15850.0320.01580.1710.00490.116325.250426.6999120.2816
296.286-0.02150.74290.04860.688410.1598-0.2165-0.353-0.37190.0453-0.01870.02640.6995-0.71040.23520.1891-0.15760.0850.38160.07920.18817.791412.0498126.0312
302.2588-0.09370.83380.6308-0.21864.431-0.0113-0.738-0.2220.11660.01860.12290.1682-1.3584-0.00730.0657-0.07740.06090.61240.06780.117312.038417.5854125.6272
311.54312.8681-1.81277.4405-2.18342.91310.6126-0.3729-0.05830.8533-0.582-0.3035-1.31560.6255-0.03061.4895-0.2521-0.3030.4808-0.04420.427943.65551.4706139.701
321.1990.1341-0.40521.3428-0.80062.2234-0.2542-0.18060.28670.3703-0.0553-0.2273-1.25780.21010.30961.0063-0.134-0.2540.1225-0.01770.352844.261248.5042125.853
330.0208-0.0839-0.0630.34780.31934.6398-0.107-0.0423-0.03490.24570.08820.1505-1.2650.11240.01880.9576-0.0171-0.13490.22460.05430.444843.450643.1404131.3781
341.4924-0.47760.63720.46020.09951.8585-0.1359-0.06170.16540.09860.0172-0.0341-0.4020.47140.11870.225-0.1371-0.03510.20350.02750.164749.586826.9871121.7802
351.11471.16370.23023.65240.24473.2317-0.39260.49340.087-0.36550.24190.2089-0.50990.64520.15070.356-0.3714-0.07910.43770.1040.183356.541334.3432109.6416
361.1960.46270.30712.52290.5332.0443-0.24450.27970.2475-0.14880.172-0.1372-0.7361.00250.07250.3074-0.3853-0.06510.51540.08480.167462.661735.0375114.2366
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 22
2X-RAY DIFFRACTION2A23 - 106
3X-RAY DIFFRACTION3A107 - 133
4X-RAY DIFFRACTION4A134 - 199
5X-RAY DIFFRACTION5A200 - 229
6X-RAY DIFFRACTION6A230 - 307
7X-RAY DIFFRACTION7B2 - 24
8X-RAY DIFFRACTION8B25 - 106
9X-RAY DIFFRACTION9B107 - 142
10X-RAY DIFFRACTION10B143 - 201
11X-RAY DIFFRACTION11B202 - 234
12X-RAY DIFFRACTION12B235 - 307
13X-RAY DIFFRACTION13C2 - 22
14X-RAY DIFFRACTION14C23 - 106
15X-RAY DIFFRACTION15C107 - 137
16X-RAY DIFFRACTION16C138 - 201
17X-RAY DIFFRACTION17C202 - 229
18X-RAY DIFFRACTION18C230 - 307
19X-RAY DIFFRACTION19D2 - 57
20X-RAY DIFFRACTION20D58 - 108
21X-RAY DIFFRACTION21D109 - 140
22X-RAY DIFFRACTION22D141 - 202
23X-RAY DIFFRACTION23D203 - 234
24X-RAY DIFFRACTION24D235 - 307
25X-RAY DIFFRACTION25E2 - 57
26X-RAY DIFFRACTION26E58 - 108
27X-RAY DIFFRACTION27E109 - 137
28X-RAY DIFFRACTION28E138 - 201
29X-RAY DIFFRACTION29E202 - 234
30X-RAY DIFFRACTION30E235 - 306
31X-RAY DIFFRACTION31F2 - 24
32X-RAY DIFFRACTION32F25 - 106
33X-RAY DIFFRACTION33F107 - 136
34X-RAY DIFFRACTION34F137 - 201
35X-RAY DIFFRACTION35F202 - 229
36X-RAY DIFFRACTION36F230 - 306

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