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Yorodumi- PDB-1enp: BRASSICA NAPUS ENOYL ACP REDUCTASE/NADH BINARY COMPLEX AT PH 8.0 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1enp | ||||||
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Title | BRASSICA NAPUS ENOYL ACP REDUCTASE/NADH BINARY COMPLEX AT PH 8.0 AND ROOM TEMPERATURE | ||||||
Components | ENOYL ACYL CARRIER PROTEIN REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / PLANT LIPID BIOSYNTHESIS | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / chloroplast / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | Brassica napus (rape) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Rafferty, J.B. / Rice, D.W. | ||||||
Citation | Journal: Structure / Year: 1995 Title: Common themes in redox chemistry emerge from the X-ray structure of oilseed rape (Brassica napus) enoyl acyl carrier protein reductase. Authors: Rafferty, J.B. / Simon, J.W. / Baldock, C. / Artymiuk, P.J. / Baker, P.J. / Stuitje, A.R. / Slabas, A.R. / Rice, D.W. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization of the Nadh-Specific Enoyl Acyl Carrier Protein Reductase from Brassica Napus Authors: Rafferty, J.B. / Simon, J.W. / Stuitje, A.R. / Slabas, A.R. / Fawcett, T. / Rice, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1enp.cif.gz | 70.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1enp.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 1enp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/1enp ftp://data.pdbj.org/pub/pdb/validation_reports/en/1enp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32977.156 Da / Num. of mol.: 1 / Mutation: S1A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brassica napus (rape) / Tissue: SEED / Gene: PEAR7 CLONE / Organ: SEED / Plasmid: PEAR2 / Gene (production host): PEAR7 CLONE / Production host: Escherichia coli (E. coli) References: UniProt: P80030, enoyl-[acyl-carrier-protein] reductase (NADH) |
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#2: Chemical | ChemComp-NAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 41 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion, hanging drop / pH: 6.2 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Apr 11, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 8364 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.043 |
Reflection | *PLUS Num. measured all: 58714 |
-Processing
Software |
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Refinement | Resolution: 2.6→10 Å / Num. reflection obs: 8364 / σ(F): 0 Details: THE STRUCTURE OF THE BINARY COMPLEX WITH NADH WAS DETERMINED BY DIFFERENCE FOURIER ANALYSIS USING DATA FROM CRYSTALS GROWN WITH NAD WHICH WERE THEN SOAKED IN NADH. THE ELECTRON DENSITY IS ...Details: THE STRUCTURE OF THE BINARY COMPLEX WITH NADH WAS DETERMINED BY DIFFERENCE FOURIER ANALYSIS USING DATA FROM CRYSTALS GROWN WITH NAD WHICH WERE THEN SOAKED IN NADH. THE ELECTRON DENSITY IS CLEARLY INTERPRETABLE FOR THE ENTIRE NADH COFACTOR INCLUDING THE NICOTINAMIDE MOIETY. THE ONLY SIGNIFICANT DIFFERENCE FROM THE STRUCTURE WITH NAD BOUND IS THE MOVEMENT OF THE SIDE CHAIN OF TYR 32 (WHICH WOULD OTHERWISE HAVE OCCUPIED SOME OF THE BINDING POCKET FOR THE NICOTINAMIDE RING) AND SMALL CHANGES ARE NOTED IN THE POSITIONS OF THE MAIN CHAIN FOR RESIDUES GLY 234, PRO 235, LEU 236, AND GLY 237. | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.132 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27 Å2 |