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Yorodumi- PDB-6ujk: Crystal Structure of a Probable short-chain type dehydrogenase/re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ujk | ||||||
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Title | Crystal Structure of a Probable short-chain type dehydrogenase/reductase (Rv1144) from Mycobacterium tuberculosis with bound NAD | ||||||
Components | Uncharacterized oxidoreductase Rv1144 | ||||||
Keywords | OXIDOREDUCTASE / SSGCID / dehydrogenase / reductase / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: to be published Title: Crystal Structure of a Probable short-chain type dehydrogenase/reductase (Rv1144) from Mycobacterium tuberculosis with bound NAD Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ujk.cif.gz | 207.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ujk.ent.gz | 163.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ujk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/6ujk ftp://data.pdbj.org/pub/pdb/validation_reports/uj/6ujk | HTTPS FTP |
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-Related structure data
Related structure data | 3pymS S: Starting model for refinement |
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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: 26845.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: Rv1144 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WGQ7, Oxidoreductases #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.12 Å3/Da / Density % sol: 42.07 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: MytuD.00554.a.B1.PW38579 at 23.33 mg/ml was incubated with 5 mM NAD, then was mixed 1:1 with MCSG1 (d9): 25% (w/v) PEG-3350, 0.1 M Tris:HCl, pH = 8.5, 0.2 M NaCl, 20% ethylene glycol cro. ...Details: MytuD.00554.a.B1.PW38579 at 23.33 mg/ml was incubated with 5 mM NAD, then was mixed 1:1 with MCSG1 (d9): 25% (w/v) PEG-3350, 0.1 M Tris:HCl, pH = 8.5, 0.2 M NaCl, 20% ethylene glycol cro. Tray: 307357d9, puck: ukh4-4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→29.96 Å / Num. obs: 141537 / % possible obs: 99.6 % / Redundancy: 6.175 % / Biso Wilson estimate: 15.064 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.047 / Χ2: 1.048 / Net I/σ(I): 23.01 / Num. measured all: 873969 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PYM Resolution: 1.2→29.96 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.64 Å2 / Biso mean: 15.5475 Å2 / Biso min: 6.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→29.96 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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