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Yorodumi- PDB-5c7h: Crystal structure of aldo-keto reductase from Sinorhizobium melil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c7h | ||||||
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Title | Crystal structure of aldo-keto reductase from Sinorhizobium meliloti 1021 in complex with NADPH | ||||||
Components | Aldo-keto reductase | ||||||
Keywords | OXIDOREDUCTASE / aldo-keto reductase / AKR / NADPH / NYSGRC / PSI-Biology / Structural Genomics / New York Structural Genomics Research Consortium | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Rhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Gasiorowska, O.A. / Shabalin, I.G. / Handing, K.B. / Seidel, R. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Funding support | United States, 1items
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Citation | Journal: to be published Title: Crystal structure of aldo-keto reductase from Sinorhizobium meliloti 1021 in complex with NADPH Authors: Gasiorowska, O.A. / Shabalin, I.G. / Handing, K.B. / Seidel, R. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c7h.cif.gz | 144.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c7h.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 5c7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c7h_validation.pdf.gz | 700.4 KB | Display | wwPDB validaton report |
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Full document | 5c7h_full_validation.pdf.gz | 700.3 KB | Display | |
Data in XML | 5c7h_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 5c7h_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/5c7h ftp://data.pdbj.org/pub/pdb/validation_reports/c7/5c7h | HTTPS FTP |
-Related structure data
Related structure data | 4xapS 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
#1: Protein | Mass: 30757.080 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria) Strain: 1021 / Gene: SMc01429 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL References: UniProt: Q92NR7, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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#2: Chemical | ChemComp-NDP / |
#3: 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: 2.24 Å3/Da / Density % sol: 45.1 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG 2 condition #28 (0.2 M Ammonium Citrate ...Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG 2 condition #28 (0.2 M Ammonium Citrate Tribasic pH 7.0, 20% (w/v) PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 1 mg/ml TEV solution at 289 K for 1 hour PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2015 / Details: Beryllium Lenses | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→50 Å / Num. all: 68811 / Num. obs: 68759 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.023 / Rrim(I) all: 0.057 / Rsym value: 0.02 / Χ2: 0.899 / Net I/av σ(I): 29.917 / Net I/σ(I): 9.2 / Num. measured all: 404374 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XAP Resolution: 1.3→50 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / WRfactor Rfree: 0.1376 / WRfactor Rwork: 0.1121 / FOM work R set: 0.9155 / SU B: 1.304 / SU ML: 0.024 / SU R Cruickshank DPI: 0.0389 / SU Rfree: 0.0377 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.038 / SU Rfree Cruickshank DPI: 0.0376 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 77.4 Å2 / Biso mean: 15.157 Å2 / Biso min: 3.86 Å2
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Refinement step | Cycle: final / Resolution: 1.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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