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Yorodumi- PDB-3oec: Crystal structure of carveol dehydrogenase from Mycobacterium the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oec | ||||||
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Title | Crystal structure of carveol dehydrogenase from Mycobacterium thermoresistibile | ||||||
Components | Carveol dehydrogenase (MythA.01326.c, A0R518 homolog) | ||||||
Keywords | OXIDOREDUCTASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / DEHYDROGENASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium thermoresistibile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors. Authors: Haft, D.H. / Pierce, P.G. / Mayclin, S.J. / Sullivan, A. / Gardberg, A.S. / Abendroth, J. / Begley, D.W. / Phan, I.Q. / Staker, B.L. / Myler, P.J. / Marathias, V.M. / Lorimer, D.D. / Edwards, T.E. #1: 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 | 3oec.cif.gz | 437.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oec.ent.gz | 357.7 KB | Display | PDB format |
PDBx/mmJSON format | 3oec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oec_validation.pdf.gz | 454.4 KB | Display | wwPDB validaton report |
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Full document | 3oec_full_validation.pdf.gz | 461.2 KB | Display | |
Data in XML | 3oec_validation.xml.gz | 47 KB | Display | |
Data in CIF | 3oec_validation.cif.gz | 69.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/3oec ftp://data.pdbj.org/pub/pdb/validation_reports/oe/3oec | HTTPS FTP |
-Related structure data
Related structure data | 3pgxC 3pxxC 3s55C 3sx2C 3t7cC 3tscC 4rgbC 5ej2C 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34275.633 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria) Strain: ATCC 19527 / NCTC 10409 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E1C9L4*PLUS, flavanone 4-reductase #2: Chemical | ChemComp-NA / #3: 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: 2.01 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 80MM NA-CACOCYLATE PH 6.5, 14.4% PEG 8000, 20% GLYCEROL, protein AT 29.5MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 12, 2010 / Details: RIGAKU VARIMAX HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 78522 / Num. obs: 77636 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 20.88 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.23 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5832 / Rsym value: 0.316 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1iy8 Resolution: 1.95→45.74 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.892 / SU B: 8.806 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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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 mean: 11.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→45.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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