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Yorodumi- PDB-2p91: Crystal structure of Enoyl-[acyl-carrier-protein] reductase (NADH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p91 | ||||||
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Title | Crystal structure of Enoyl-[acyl-carrier-protein] reductase (NADH) from Aquifex aeolicus VF5 | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE / NADH-dependent enoyl-ACP reductase / aq_1552 / fabI / Aquifex aeolicus VF5 / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / identical protein binding Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chen, L. / Li, Y. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhao, M. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Enoyl-[acyl-carrier-protein] reductase (NADH) from Aquifex aeolicus VF5 Authors: Chen, L. / Li, Y. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhao, M. / Rose, J.P. / Wang, B.-C. | ||||||
History |
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Remark 999 | SEQUENCE AUTHORS STATE THAT THE PRESENCE OF N-TERMINAL 15 AMINO ACIDS RESIDUES IS DERIVED FROM THE ... SEQUENCE AUTHORS STATE THAT THE PRESENCE OF N-TERMINAL 15 AMINO ACIDS RESIDUES IS DERIVED FROM THE DIFFERENCE IN GENOME ANNOTATION BETWEEN UNIPROT AND GENBANK SEQUENCES. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p91.cif.gz | 206.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p91.ent.gz | 164.5 KB | Display | PDB format |
PDBx/mmJSON format | 2p91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/2p91 ftp://data.pdbj.org/pub/pdb/validation_reports/p9/2p91 | HTTPS FTP |
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-Related structure data
Related structure data | 1jw7 S: Starting model for refinement |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a tetramer in the asymmetric unit. |
-Components
#1: Protein | Mass: 31536.371 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: fabI, aq_1552 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL References: UniProt: O67505, 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: 2.03 Å3/Da / Density % sol: 39.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10.93 mg/ml) AND RESERVOIR SOLUTION CONTAINING 0.1 M Phosphate-citrate (pH 4.2), 40% v/v PEG200, 0.15 M Sodium ...Details: USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (10.93 mg/ml) AND RESERVOIR SOLUTION CONTAINING 0.1 M Phosphate-citrate (pH 4.2), 40% v/v PEG200, 0.15 M Sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97243 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97243 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 70158 / % possible obs: 99.9 % / Redundancy: 11.1 % / Rsym value: 0.089 / Χ2: 1.44 / Net I/σ(I): 10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1JW7 1jw7 Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 18.638 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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