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Yorodumi- PDB-2wyv: High resolution structure of Thermus thermophilus enoyl-acyl carr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wyv | ||||||
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Title | High resolution structure of Thermus thermophilus enoyl-acyl carrier protein reductase NAD-form | ||||||
Components | ENOYL-[ACYL CARRIER PROTEIN] REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / FATTY ACID BIOSYNTHESIS / OXIDATION REDUCTION | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Otero, J.M. / Noel, A.J. / Guardado-Calvo, P. / Llamas-Saiz, A.L. / van Raaij, M.J. | ||||||
Citation | Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2012 Title: High-resolution structures of Thermus thermophilus enoyl-acyl carrier protein reductase in the apo form, in complex with NAD+ and in complex with NAD+ and triclosan. Authors: Otero, J.M. / Noel, A.J. / Guardado-Calvo, P. / Llamas-Saiz, A.L. / Wende, W. / Schierling, B. / Pingoud, A. / van Raaij, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wyv.cif.gz | 213.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wyv.ent.gz | 171.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/2wyv ftp://data.pdbj.org/pub/pdb/validation_reports/wy/2wyv | HTTPS FTP |
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-Related structure data
Related structure data | 2wyuSC 2wywC C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 28141.432 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 Description: THERMUS THERMOPHILUS DNA OBTAINED FROM PROF. WOLFGANG LIEBL, GOETTINGEN. Plasmid: PET30A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: Q5SLI9, EC: 1.3.1.10 #2: Chemical | #3: Chemical | #4: 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: 2.2 Å3/Da / Density % sol: 44.7 % / Description: NONE |
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Crystal grow | pH: 5.4 Details: 20% (W/V) POLYETHYLENE GLYCOL 4000, 100 MM SODIUM CITRATE PH 5.4, 2 MM NAD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 19, 2008 / Details: TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: SINGLE SILICON (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40 Å / Num. obs: 77770 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.2 / % possible all: 89.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WYU Resolution: 1.86→39.75 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.043 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.15 / 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 mean: 22.445 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→39.75 Å
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Refine LS restraints |
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