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- PDB-4zp1: Crystal structure of Zymomonas mobilis pyruvate decarboxylase var... -

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Basic information

Entry
Database: PDB / ID: 4zp1
TitleCrystal structure of Zymomonas mobilis pyruvate decarboxylase variant Glu473Ala
ComponentsPyruvate decarboxylase
KeywordsLYASE / thiamin diphosphate (ThDP) / pyruvate decarboxylase
Function / homology
Function and homology information


pyruvate decarboxylase / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding / cytosol
Similarity search - Function
: / : / Thiamine pyrophosphate (TPP)-dependent enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding ...: / : / Thiamine pyrophosphate (TPP)-dependent enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / THIAMINE DIPHOSPHATE / Pyruvate decarboxylase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.205 Å
AuthorsWechsler, C. / Neumann, P. / Tittmann, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFOR 1296/TP3 Germany
CitationJournal: Chembiochem / Year: 2015
Title: Tuning and Switching Enantioselectivity of Asymmetric Carboligation in an Enzyme through Mutational Analysis of a Single Hot Spot.
Authors: Wechsler, C. / Meyer, D. / Loschonsky, S. / Funk, L.M. / Neumann, P. / Ficner, R. / Brodhun, F. / Muller, M. / Tittmann, K.
History
DepositionMay 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate decarboxylase
B: Pyruvate decarboxylase
C: Pyruvate decarboxylase
D: Pyruvate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,82916
Polymers243,7294
Non-polymers2,10012
Water10,935607
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28350 Å2
ΔGint-207 kcal/mol
Surface area64890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.290, 167.640, 110.820
Angle α, β, γ (deg.)90.00, 101.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pyruvate decarboxylase / / PDC


Mass: 60932.289 Da / Num. of mol.: 4 / Mutation: E473A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: pdc, ZMO1360 / Production host: Escherichia coli (E. coli) / References: UniProt: P06672, pyruvate decarboxylase

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Non-polymers , 5 types, 619 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ZmPDC variant Glu473Ala was concentrated to 7.5 mg/mL in 10 mM citrate buffer (pH 6.0) containing 1 mM ThDP and 1 mM MgSO4. 1 microL of the enzyme was mixed with 1 microL of the reservoir ...Details: ZmPDC variant Glu473Ala was concentrated to 7.5 mg/mL in 10 mM citrate buffer (pH 6.0) containing 1 mM ThDP and 1 mM MgSO4. 1 microL of the enzyme was mixed with 1 microL of the reservoir solution containing 100 mM Tris, 40 mM NiCl2, 15% PEG2000, 1 mM ThDP, 1 mM MgSO4, and 100 mM sodium malonate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9842 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9842 Å / Relative weight: 1
ReflectionResolution: 2.2→47.55 Å / Num. all: 124039 / Num. obs: 124039 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 37.43 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.071 / Χ2: 1.009 / Net I/σ(I): 16.15 / Num. measured all: 471480
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.2-2.313.70.8030.5592.385563815666152080.65697.1
2.31-2.40.8940.4343.195143313149130290.50299.1
2.4-2.610.9370.34.457914520708204640.34898.8
2.61-3.380.9930.10511.1315627141599409050.12298.3
3.38-3.780.9980.04226.234650972594670.04997.3
3.78-4.160.9990.03136.8725301644363960.03699.3
4.16-4.550.9990.02543.5116897444044070.02999.3
4.55-140.9990.021495054613958136830.02498
14-170.9990.01478.438392252230.01699.1
17-500.9990.01562.247602802570.01891.8
5016

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.205→47.545 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 6195 5 %Random selection
Rwork0.1698 ---
obs0.1721 123937 98.26 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.205→47.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17048 0 122 607 17777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00517645
X-RAY DIFFRACTIONf_angle_d0.84424017
X-RAY DIFFRACTIONf_dihedral_angle_d12.4416321
X-RAY DIFFRACTIONf_chiral_restr0.0322670
X-RAY DIFFRACTIONf_plane_restr0.0033127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.205-2.23010.34482020.29363832X-RAY DIFFRACTION97
2.2301-2.25630.34442010.28763818X-RAY DIFFRACTION95
2.2563-2.28380.31692020.26993858X-RAY DIFFRACTION97
2.2838-2.31270.3162070.25263947X-RAY DIFFRACTION99
2.3127-2.34320.30412080.24673957X-RAY DIFFRACTION98
2.3432-2.37530.29942060.24113917X-RAY DIFFRACTION99
2.3753-2.40920.27112070.23933934X-RAY DIFFRACTION99
2.4092-2.44510.30822080.23053938X-RAY DIFFRACTION99
2.4451-2.48340.29322070.21983946X-RAY DIFFRACTION99
2.4834-2.52410.27612090.21743981X-RAY DIFFRACTION99
2.5241-2.56760.26892060.21143900X-RAY DIFFRACTION99
2.5676-2.61430.28782060.20143925X-RAY DIFFRACTION98
2.6143-2.66450.25772070.20453921X-RAY DIFFRACTION98
2.6645-2.71890.27852060.20453914X-RAY DIFFRACTION97
2.7189-2.7780.26981980.20493753X-RAY DIFFRACTION95
2.778-2.84270.28052090.21493964X-RAY DIFFRACTION99
2.8427-2.91370.25972080.20993956X-RAY DIFFRACTION99
2.9137-2.99250.26582080.19673945X-RAY DIFFRACTION99
2.9925-3.08060.23492080.20193957X-RAY DIFFRACTION99
3.0806-3.180.2652080.19373955X-RAY DIFFRACTION99
3.18-3.29360.24622070.18353928X-RAY DIFFRACTION99
3.2936-3.42540.21532070.17543934X-RAY DIFFRACTION99
3.4254-3.58130.22692040.17393871X-RAY DIFFRACTION97
3.5813-3.770.20472050.14843896X-RAY DIFFRACTION98
3.77-4.00610.17312090.13683973X-RAY DIFFRACTION99
4.0061-4.31520.1562090.12023982X-RAY DIFFRACTION99
4.3152-4.74910.14412100.11253986X-RAY DIFFRACTION99
4.7491-5.43550.17162020.12793868X-RAY DIFFRACTION96
5.4355-6.84490.17462110.1444006X-RAY DIFFRACTION100
6.8449-47.5560.15032100.12993980X-RAY DIFFRACTION98
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)
11.62010.621-0.66192.0941-0.10510.8783-0.01470.0118-0.05440.24860.03-0.61210.08480.1741-0.0170.3580.0341-0.16170.3278-0.01740.475719.0890.9601129.8881
20.56340.29380.05541.45630.47591.44790.18260.109-0.0917-0.12270.0713-0.55490.00050.1722-0.2440.29690.0148-0.03620.3408-0.03460.535218.91441.1757118.6001
31.50270.08980.53360.7714-0.44050.46-0.10860.047-0.3020.19760.0672-0.0259-0.16420.01110.04140.35160.0151-0.00470.319-0.03150.35565.828223.5953123.6866
40.93560.1961-0.0322.4182-0.39611.6590.0104-0.0455-0.01470.27980.08530.17170.0345-0.2547-0.09670.33180.01490.03740.3950.0230.2729-14.357617.0868131.412
50.63210.2825-0.44711.6792-0.32430.73720.0278-0.1298-0.16430.58920.0503-0.11820.1795-0.116-0.07720.66680.0072-0.09320.4260.01490.2574-2.4745-5.9426146.4155
61.75470.18040.93661.59430.43411.16630.04510.0402-0.22820.36960.01310.20540.2582-0.129-0.02890.5036-0.08050.00680.46990.0570.2864-12.5194-8.3543136.3121
71.49820.2604-0.03931.8298-0.06091.8877-0.0103-0.0822-0.14590.23460.0517-0.20290.2077-0.1391-0.0320.3812-0.01260.00540.30850.03650.2976-2.8287-25.3695121.636
80.60960.5185-0.01212.14880.70241.35220.03910.05020.0798-0.05450.027-0.2057-0.079-0.062-0.06130.294-0.0009-0.02260.26070.01010.2643-0.6331-14.3232113.9832
90.9832-0.30210.22480.44620.0470.8028-0.0389-0.05820.01770.10080.1711-0.59820.19430.1694-0.12090.4410.0794-0.08570.3861-0.11820.88229.858-35.384109.9911
100.2674-0.0098-0.29270.53170.45020.97530.0627-0.0749-0.18830.23290.1247-0.49860.17690.2422-0.1440.48170.0802-0.18340.3646-0.03360.8225.512-30.9954123.089
110.7333-0.60690.61472.3646-0.14470.9649-0.0662-0.1901-0.20650.49280.0384-0.660.19820.14060.03590.77330.0479-0.24050.42920.06620.660716.8974-24.6411143.7938
122.51650.722-1.14170.918-0.04581.3437-0.0147-0.13760.20130.28840.2324-0.5030.03760.2802-0.21030.59790.0349-0.33920.4839-0.02471.063830.0147-19.5456132.4691
131.4169-0.29060.69671.96-0.06020.68980.02870.04090.0291-0.24870.0364-0.5428-0.05870.1424-0.0660.3889-0.01930.16810.358-0.02580.479719.8279-6.839787.4278
140.7430.19320.0242.15420.50461.19260.1117-0.1690.1374-0.09490.0594-0.7957-0.04270.1112-0.16880.2807-0.01210.06470.3003-0.0360.514619.2454-7.120298.6509
150.0624-0.2234-0.07051.59-0.35880.51780.1614-0.0642-0.1406-0.08630.0126-0.07560.2319-0.0936-0.16240.3567-0.03270.00580.3574-0.07060.2760.3587-29.297591.5017
161.15810.26630.16722.1506-0.35920.1714-0.09320.0805-0.0244-0.22630.13220.2324-0.0588-0.218-0.03320.3579-0.0004-0.02560.46390.03460.2538-13.7967-19.031283.1817
172.0889-0.1963-0.12682.6081-1.05512.13440.0670.1392-0.2582-0.1002-0.03180.18870.4024-0.2215-0.01520.3678-0.06190.01020.3603-0.02180.3299-11.2228-30.224187.9035
180.7954-0.10330.0640.956-0.57440.73130.08810.15480.0762-0.33680.05310.0417-0.0335-0.1758-0.15130.564-0.0050.0370.44170.03750.2695-5.7243-6.871570.9055
190.3192-0.60410.38722.20730.33541.44050.04460.22720.1446-0.4545-0.0538-0.0314-0.2157-0.05140.01380.5954-0.01950.15030.4280.0590.33653.41256.49872.1839
201.62250.5758-1.11641.58170.50581.3982-0.16810.03490.2004-0.51820.10920.14720.0541-0.09940.04410.56970.13640.02250.49250.10680.3193-8.35912.556973.0605
211.8099-0.3651-0.44912.180.42311.5634-0.01310.06890.0373-0.16870.011-0.1527-0.0915-0.09770.00130.29870.00130.02170.27190.01450.2396-0.874114.877596.3275
220.7025-0.9847-0.19622.40840.74681.1993-0.01880.0167-0.07120.07280.0519-0.16990.1776-0.034-0.02050.2858-0.01170.0470.26770.01220.2413-1.84428.6412104.9324
230.49240.2374-0.08920.61680.26681.0856-0.09720.1225-0.0969-0.09120.0942-0.4254-0.02890.1574-0.00210.3603-0.03390.05840.3878-0.05060.781829.563727.0676109.2344
240.2056-0.03250.23320.43610.6681.3945-0.02970.17640.0686-0.46020.1326-0.7864-0.6730.6359-0.02610.5888-0.17030.26610.6232-0.02960.969239.826933.432290.9599
251.29920.17910.19320.35360.22321.38650.01690.10450.4635-0.29970.062-0.3975-0.24270.192-0.08310.5146-0.03380.1970.36340.01830.729819.546923.782485.2908
260.91080.3979-1.05852.443-0.01871.3023-0.0415-0.01910.2183-0.44550.096-0.6534-0.0390.0603-0.04430.6692-0.03170.26890.42510.01780.598717.453816.259273.945
271.41080.16240.65151.7381-0.31531.5606-0.02950.1889-0.2659-0.57840.2258-0.4555-0.06040.359-0.16890.6211-0.03270.34250.51310.00870.856828.669117.608881.8789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 110 )
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 170 )
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 206 )
4X-RAY DIFFRACTION4chain 'A' and (resid 207 through 348 )
5X-RAY DIFFRACTION5chain 'A' and (resid 349 through 527 )
6X-RAY DIFFRACTION6chain 'A' and (resid 528 through 566 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 64 )
8X-RAY DIFFRACTION8chain 'B' and (resid 65 through 180 )
9X-RAY DIFFRACTION9chain 'B' and (resid 181 through 283 )
10X-RAY DIFFRACTION10chain 'B' and (resid 284 through 455 )
11X-RAY DIFFRACTION11chain 'B' and (resid 456 through 527 )
12X-RAY DIFFRACTION12chain 'B' and (resid 528 through 566 )
13X-RAY DIFFRACTION13chain 'C' and (resid 2 through 110 )
14X-RAY DIFFRACTION14chain 'C' and (resid 111 through 170 )
15X-RAY DIFFRACTION15chain 'C' and (resid 171 through 216 )
16X-RAY DIFFRACTION16chain 'C' and (resid 217 through 307 )
17X-RAY DIFFRACTION17chain 'C' and (resid 308 through 347 )
18X-RAY DIFFRACTION18chain 'C' and (resid 348 through 432 )
19X-RAY DIFFRACTION19chain 'C' and (resid 433 through 507 )
20X-RAY DIFFRACTION20chain 'C' and (resid 508 through 566 )
21X-RAY DIFFRACTION21chain 'D' and (resid 2 through 110 )
22X-RAY DIFFRACTION22chain 'D' and (resid 111 through 180 )
23X-RAY DIFFRACTION23chain 'D' and (resid 181 through 334 )
24X-RAY DIFFRACTION24chain 'D' and (resid 335 through 366 )
25X-RAY DIFFRACTION25chain 'D' and (resid 367 through 455 )
26X-RAY DIFFRACTION26chain 'D' and (resid 456 through 514 )
27X-RAY DIFFRACTION27chain 'D' and (resid 515 through 566 )

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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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