+Open data
-Basic information
Entry | Database: PDB / ID: 1gyr | ||||||
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Title | Mutant form of enoyl thioester reductase from Candida tropicalis | ||||||
Components | 2,4-DIENOYL-COA REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information trans-2-enoyl-CoA reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADPH) / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid metabolic process / fatty acid biosynthetic process / mitochondrion Similarity search - Function | ||||||
Biological species | CANDIDA TROPICALIS (yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Airenne, T.T. / Torkko, J.M. / Van Der Plas, S. / Sormunen, R.T. / Kastaniotis, A.J. / Wierenga, R.K. / Hiltunen, J.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structure-Function Analysis of Enoyl Thioester Reductase Involved in Mitochondrial Maintenance Authors: Airenne, T.T. / Torkko, J.M. / Van Der Plas, S. / Sormunen, R.T. / Kastaniotis, A.J. / Wierenga, R.K. / Hiltunen, J.K. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gyr.cif.gz | 218.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gyr.ent.gz | 176.8 KB | Display | PDB format |
PDBx/mmJSON format | 1gyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/1gyr ftp://data.pdbj.org/pub/pdb/validation_reports/gy/1gyr | HTTPS FTP |
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-Related structure data
Related structure data | 1gu7SC 1gufC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | CHAINS A AND B FORM A CLOSE CONTACT IN THE CRYSTAL, VIA BETA SHEET INTERACTIONS BETWEEN STRAND AD OF CHAIN A AND STRAND AD OF CHAIN B . CHAIN C FORMS SIMILAR INTERACTIONS WITH ANOTHER CRYSTAL-SYMMETRY RELATED CHAIN. |
-Components
#1: Protein | Mass: 39506.332 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CANDIDA TROPICALIS (yeast) / Strain: PK233 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): BJ1991 / References: UniProt: Q8WZM3 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 3.17 Å3/Da / Density % sol: 61.24 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 44923 / % possible obs: 98.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 6.9 / % possible all: 90.3 |
Reflection | *PLUS Lowest resolution: 20 Å / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS Lowest resolution: 2.69 Å / % possible obs: 90.3 % / Num. unique obs: 4364 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GU7 Resolution: 2.6→19.96 Å / SU B: 10.347 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.527 / ESU R Free: 0.294 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 27.948 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.96 Å
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Refinement | *PLUS Num. reflection obs: 44923 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.193 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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