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Yorodumi- PDB-3gvc: Crystal structure of probable short-chain dehydrogenase-reductase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gvc | ||||||
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Title | Crystal structure of probable short-chain dehydrogenase-reductase from Mycobacterium tuberculosis | ||||||
Components | Probable short-chain type dehydrogenase/reductase | ||||||
Keywords | OXIDOREDUCTASE / SSGCID / deCODE / NIAID / UWPPG / SBRI / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Tuberculosis (Edinb) / Year: 2015 Title: Increasing the structural coverage of tuberculosis drug targets. Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gvc.cif.gz | 185.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gvc.ent.gz | 147.2 KB | Display | PDB format |
PDBx/mmJSON format | 3gvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/3gvc ftp://data.pdbj.org/pub/pdb/validation_reports/gv/3gvc | HTTPS FTP |
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-Related structure data
Related structure data | 3gvgC 3gwcC 3h7fC 3h81C 3he2C 3hwiC 3hwkC 3hzgC 3icoC 3khpC 3llsC 3moyC 3mpzC 3mybC 3ndnC 3ndoC 3nf4C 3ng3C 3njdC 3nwoC 3o0mC 3o38C 3oc6C 3oc7C 3oi9C 3oksC 3omeC 3p0tC 3p2yC 3p4iC 3p4tC 3p5mC 3p85C 3pe8C 3pk0C 3ppiC 3pzyC 3q1tC 3q8nC 3qbpC 3qdfC 3qhaC 3qivC 3qk8C 3qkaC 3qljC 3qmjC 3qreC 3quaC 3quvC 3qxiC 3qxzC 3qyrC 3r0oC 3r1iC 3r1jC 3r20C 3r2nC 3r4tC 3r6hC 3r6oC 3r7kC 3r8cC 3r9pC 3r9qC 3r9rC 3r9sC 3r9tC 3rd5C 3rd7C 3rd8C 3rfqC 3rihC 3rr2C 3rr6C 3rrpC 3rrvC 3rsiC 3rv2C 3s82C 3sbxC 3sf6C 3sllC 3svkC 3svtC 3swoC 3swtC 3swxC 3t3wC 3tavC 3tcrC 3tdeC 3tjrC 3tl3C 3tlfC 3trrC 3tx2C 3tzqC 3tzuC 3u0aC 3u0bC 3ucxC 3uveC 4di1C 4dieC 4dq8C 4dxlC 4ed4C 4egeC 4egfC 4emdC 4eo9C 4eyeC 4f3wC 4f47C 4ffcC 4gk6C 4hdtC 4hr3C 4i1yC 4ijnC 4iv6C 4iz9C 4j5iC 4kamC 4lgvC 4o2dC 1iy8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28146.250 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Expressed with an N-terminal hexahis tag fused with a 3C protease substrate linker but not-cleaved prior to crystallization Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT1991, Rv1941 / Production host: Escherichia coli (E. coli) References: UniProt: P95273, UniProt: I6XZC4*PLUS, Oxidoreductases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Emerald Wizard Full screen condition F6, 20% PEG 3000, 0.1 M Tris, 0.2 M CaCl2, 11.8 mg/mL protein, crystal ID 202293f6, 25% glycerol as cryo-protectant, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97933 Å |
Detector | Date: Mar 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. obs: 36246 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.734 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 7.97 |
Reflection shell | Resolution: 2.45→2.51 Å / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.2 / Num. measured obs: 7568 / Num. unique all: 2654 / Num. unique obs: 2654 / % possible all: 99.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IY8 Resolution: 2.45→19.9 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.83 / SU B: 9.386 / SU ML: 0.211 / SU R Cruickshank DPI: 0.549 / SU Rfree: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.548 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.25 Å2 / Biso mean: 25.165 Å2 / Biso min: 4.34 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.514 Å / Total num. of bins used: 20
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