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- PDB-3gvc: Crystal structure of probable short-chain dehydrogenase-reductase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gvc | ||||||
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Title | Crystal structure of probable short-chain dehydrogenase-reductase from Mycobacterium tuberculosis | ||||||
![]() | Probable short-chain type dehydrogenase/reductase | ||||||
![]() | OXIDOREDUCTASE / SSGCID / deCODE / NIAID / UWPPG / SBRI / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185.2 KB | Display | ![]() |
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PDB format | ![]() | 147.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.4 KB | Display | ![]() |
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Full document | ![]() | 469.4 KB | Display | |
Data in XML | ![]() | 36.6 KB | Display | |
Data in CIF | ![]() | 51.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ![]() 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 ( |
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Similar structure data | |
Other databases |
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Links
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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.) ![]() ![]() ![]() ![]() References: UniProt: P95273, UniProt: I6XZC4*PLUS, Oxidoreductases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() 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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