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Yorodumi- PDB-3moy: Crystal structure of probable enoyl-CoA hydratase from Mycobacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3moy | ||||||
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Title | Crystal structure of probable enoyl-CoA hydratase from Mycobacterium smegmatis | ||||||
Components | Probable enoyl-CoA hydratase | ||||||
Keywords | LYASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / enoyl CoA / Actinobacteria | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 | 3moy.cif.gz | 122.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3moy.ent.gz | 94.2 KB | Display | PDB format |
PDBx/mmJSON format | 3moy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/3moy ftp://data.pdbj.org/pub/pdb/validation_reports/mo/3moy | HTTPS FTP |
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-Related structure data
Related structure data | 3gvcC 3gvgC 3gwcC 3h7fC 3h81SC 3he2C 3hwiC 3hwkC 3hzgC 3icoC 3khpC 3llsC 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 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28064.943 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084/ mc(2)155 / Gene: MSMEG_6777 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R747, enoyl-CoA hydratase |
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-Non-polymers , 6 types, 239 molecules
#2: Chemical | ChemComp-SO4 / | ||||||
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#3: Chemical | ChemComp-TRS / | ||||||
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: JCSG+ screen condition D7, 40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4 with 20% ethylene glycol as cryo-protectant, 41.4 mg/mL protein in Tris buffer with 0.3 M NaCl and 10% glycerol, ...Details: JCSG+ screen condition D7, 40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4 with 20% ethylene glycol as cryo-protectant, 41.4 mg/mL protein in Tris buffer with 0.3 M NaCl and 10% glycerol, crystal tracking ID 215265d7, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97946 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→35.29 Å / Num. obs: 41710 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.07 % / Biso Wilson estimate: 24.77 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 8.94 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 3.8 / Num. measured obs: 27548 / Num. unique obs: 3082 / % possible all: 99.8 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 49.15 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3H81 Resolution: 1.5→35.29 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.16 / WRfactor Rwork: 0.151 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.91 / SU B: 2.215 / SU ML: 0.038 / SU R Cruickshank DPI: 0.064 / SU Rfree: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 63.4 Å2 / Biso mean: 20.39 Å2 / Biso min: 9.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→35.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 42.1833 Å / Origin y: 42.888 Å / Origin z: 30.2572 Å
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