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Yorodumi- PDB-3tsc: Crystal structure of short chain dehydrogenase MAP_2410 from Myco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tsc | ||||||
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Title | Crystal structure of short chain dehydrogenase MAP_2410 from Mycobacterium paratuberculosis bound to NAD | ||||||
Components | Putative oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / nucleotide / adenine dinucleotide / short chain dehydrogenase / SRD family protein / carveol dehydrogenase / ortholog | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium avium subsp. paratuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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 | 3tsc.cif.gz | 399.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tsc.ent.gz | 327.7 KB | Display | PDB format |
PDBx/mmJSON format | 3tsc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tsc_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3tsc_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3tsc_validation.xml.gz | 45.7 KB | Display | |
Data in CIF | 3tsc_validation.cif.gz | 65.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/3tsc ftp://data.pdbj.org/pub/pdb/validation_reports/ts/3tsc | HTTPS FTP |
-Related structure data
Related structure data | 3oecC 3pgxSC 3pxxC 3s55C 3sx2C 3t7cC 4rgbC 5ej2C 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
#1: Protein | Mass: 29133.008 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria) Gene: MAP_2410 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73X99 #2: Chemical | ChemComp-NAD / #3: Chemical | #4: 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: 2.13 Å3/Da / Density % sol: 42.38 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MypaA.01326.g.A1 PW29476 at 27.6 mg/mL against JCSG+ D5, 70% MPD, 0.1 M Hepes pH 7.5, crystal tracking ID 220650d3, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→50 Å / Num. all: 61220 / Num. obs: 60295 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 21.616 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.54 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | 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 3pgx Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.1844 / WRfactor Rwork: 0.141 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8636 / SU B: 8.124 / SU ML: 0.117 / SU R Cruickshank DPI: 0.2164 / SU Rfree: 0.1751 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 43.82 Å2 / Biso mean: 14.8272 Å2 / Biso min: 4.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 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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