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Yorodumi- PDB-3sx2: Crystal structure of a putative 3-ketoacyl-(acyl-carrier-protein)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sx2 | ||||||
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Title | Crystal structure of a putative 3-ketoacyl-(acyl-carrier-protein) reductase from Mycobacterium paratuberculosis in complex with NAD | ||||||
Components | Putative 3-ketoacyl-(acyl-carrier-protein) reductase | ||||||
Keywords | OXIDOREDUCTASE / SSGCID / 3-KETOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE / MYCOBACERIUM PARATUBERCULOSIS / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / putative 3-KETOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium avium subsp. paratuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.5 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 | 3sx2.cif.gz | 817 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sx2.ent.gz | 680 KB | Display | PDB format |
PDBx/mmJSON format | 3sx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/3sx2 ftp://data.pdbj.org/pub/pdb/validation_reports/sx/3sx2 | HTTPS FTP |
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-Related structure data
Related structure data | 3oecSC 3pgxC 3pxxC 3s55C 3t7cC 3tscC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28592.520 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria) Strain: ATCC BAA-968/K-10 / Gene: MAP_2861 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q73W00 #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-MPD / ( #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: 2.49 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: EBS JCSG+ SCREEN D5 OPTIMIZED TO: 100MM HEPES PH 6.5, 70% MPD; MYPAA.01326.D.A1 PW29473 AT 23MG/ ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976484 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2010 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976484 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. all: 351856 / Num. obs: 333445 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 21.16 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 21.04 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 4.1 / Num. unique all: 26062 / Rsym value: 0.304 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: PDB entry 3oec modified with CCP4 program CHAINSAW Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.882 / SU ML: 0.032 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.058 / 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: 11.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.54 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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