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- PDB-3o0k: Crystal structure of ALDO/KETO reductase from brucella melitensis -
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Open data
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Basic information
Entry | Database: PDB / ID: 3o0k | ||||||
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Title | Crystal structure of ALDO/KETO reductase from brucella melitensis | ||||||
![]() | Aldo/keto reductase | ||||||
![]() | OXIDOREDUCTASE / SSGCID / ALS COLLABORATIVE CRYSTALLOGRAPHY / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | ![]() Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Crystal structure of ALDO/KETO reductase from brucella melitensis Authors: SSGCID / Abendroth, J. / Edwards, T.E. / Staker, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 431.9 KB | Display | ![]() |
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PDB format | ![]() | 355.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.2 KB | Display | ![]() |
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Full document | ![]() | 483 KB | Display | |
Data in XML | ![]() | 44.4 KB | Display | |
Data in CIF | ![]() | 65.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mzrS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31711.936 Da / Num. of mol.: 4 / Fragment: UNP residues 19-279 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q2YII2, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.28 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: EBS JCSG+ SCREEN, D9: 0.17M AMMONIUM SULPHATE, 25.5% PEG 4000, 15% GLYCEROL; BRABA.00019.A AT 73MG/ML, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 28, 2010 / Details: Rigaku/Osmic 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: 1.8→50 Å / Num. all: 87518 / Num. obs: 87040 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 23.54 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.65 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6314 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1mzr, residues 1-220, modified with CCP4 program CHAINSAW Resolution: 1.8→46.51 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.92 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.137 / 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: 13.76 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→46.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 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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