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Yorodumi- PDB-3grk: Crystal structure of short chain dehydrogenase reductase SDR gluc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3grk | ||||||
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Title | Crystal structure of short chain dehydrogenase reductase SDR glucose-ribitol dehydrogenase from Brucella melitensis | ||||||
Components | Enoyl-(acyl-carrier-protein) reductase (NADH) | ||||||
Keywords | OXIDOREDUCTASE / SSGCID / NIAID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | Brucella melitensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of short chain dehydrogenase reductase SDR glucose-ribitol dehydrogenase from Brucella melitensis Authors: Edwards, T.E. / Staker, B.L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3grk.cif.gz | 382.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3grk.ent.gz | 311.6 KB | Display | PDB format |
PDBx/mmJSON format | 3grk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3grk_validation.pdf.gz | 507 KB | Display | wwPDB validaton report |
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Full document | 3grk_full_validation.pdf.gz | 531.4 KB | Display | |
Data in XML | 3grk_validation.xml.gz | 72.6 KB | Display | |
Data in CIF | 3grk_validation.cif.gz | 100.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/3grk ftp://data.pdbj.org/pub/pdb/validation_reports/gr/3grk | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 31530.762 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: Expressed with a N-terminal hexahis tag and 3C protease cleavage site but crystallized protein was not cleaved Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: biovar Abortus 2308 / Gene: BMEI1512 / Production host: Escherichia coli (E. coli) References: UniProt: Q8YFK8, enoyl-[acyl-carrier-protein] reductase (NADH) #2: 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: 2.14 Å3/Da / Density % sol: 42.49 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PACT Premier screen condition C11, 20% PEG 6000, 0.2 M CaCl2, 0.1 M HEPES NaOH pH 7.0, 47.3 mg/mL protein, crystal ID 200296c11, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 2, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→20 Å / Num. obs: 84019 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.157 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.35→2.41 Å / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3.6 / Num. measured obs: 16977 / Num. unique all: 5125 / Num. unique obs: 5125 / % possible all: 79.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→19.81 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.833 / SU B: 8.008 / SU ML: 0.192 / SU R Cruickshank DPI: 0.48 / SU Rfree: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.479 / ESU R Free: 0.289 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.06 Å2 / Biso mean: 27.873 Å2 / Biso min: 5.39 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.41 Å / Total num. of bins used: 20
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