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Yorodumi- PDB-3dlp: 4-Chlorobenzoyl-CoA Ligase/Synthetase, Mutant D402P, bound to 4CB -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dlp | ||||||
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Title | 4-Chlorobenzoyl-CoA Ligase/Synthetase, Mutant D402P, bound to 4CB | ||||||
Components | 4-Chlorobenzoate CoA Ligase/Synthetase | ||||||
Keywords | LIGASE / Adenylate-forming enzymes Acyl-CoA ligase Domain Alternation | ||||||
Function / homology | Function and homology information medium-chain fatty acid-CoA ligase activity / fatty acid metabolic process / nucleotide binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Alcaligenes sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Wu, R. / Cao, J. / Reger, A.S. / Lu, X. / Gulick, A.M. / Dunaway-Mariano, D. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: The mechanism of domain alternation in the acyl-adenylate forming ligase superfamily member 4-chlorobenzoate: coenzyme A ligase Authors: Wu, R. / Reger, A.S. / Lu, X. / Gulick, A.M. / Dunaway-Mariano, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dlp.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dlp.ent.gz | 80.2 KB | Display | PDB format |
PDBx/mmJSON format | 3dlp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/3dlp ftp://data.pdbj.org/pub/pdb/validation_reports/dl/3dlp | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 54363.137 Da / Num. of mol.: 1 / Mutation: D402P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes sp. (bacteria) / Strain: AL3007 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8GN86*PLUS, EC: 6.2.1.33 |
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#2: Chemical | ChemComp-174 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 Details: 16-24% pentaerythritol propoxylate 426 0.1 M HEPES 1mM ATP 1mM 4CB, pH 6.5, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 19751 / % possible obs: 94.8 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.6→2.667 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.6 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IT5D Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 23.845 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.565 / ESU R Free: 0.305 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.908 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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