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Yorodumi- PDB-4rlf: Crystal structure of a benzoate coenzyme A ligase with p-Toluic a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rlf | ||||||
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Title | Crystal structure of a benzoate coenzyme A ligase with p-Toluic acid and o-Toluic acid | ||||||
Components | Benzoate-coenzyme A ligase | ||||||
Keywords | LIGASE / Substrate Specificity / Kinetics | ||||||
Function / homology | Function and homology information acid-thiol ligase activity / CoA-ligase activity / secondary metabolite biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Strom, S. / Nosrati, M. / Thornburg, C. / Walker, K. / Geiger, J.H. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Kinetically and Crystallographically Guided Mutations of a Benzoate CoA Ligase (BadA) Elucidate Mechanism and Expand Substrate Permissivity. Authors: Thornburg, C.K. / Wortas-Strom, S. / Nosrati, M. / Geiger, J.H. / Walker, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rlf.cif.gz | 219.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rlf.ent.gz | 173 KB | Display | PDB format |
PDBx/mmJSON format | 4rlf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rlf_validation.pdf.gz | 486.5 KB | Display | wwPDB validaton report |
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Full document | 4rlf_full_validation.pdf.gz | 498.7 KB | Display | |
Data in XML | 4rlf_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 4rlf_validation.cif.gz | 63.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/4rlf ftp://data.pdbj.org/pub/pdb/validation_reports/rl/4rlf | HTTPS FTP |
-Related structure data
Related structure data | 4eatC 4rlqC 4rm2C 4rm3C 4rmnC 4zjzC 2v7bS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 56333.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Gene: badA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q93TK0 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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: 2.3 Å3/Da / Density % sol: 46.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15 % PEG 3350, 0.1 M Tris pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→50 Å / Num. obs: 96640 / % possible obs: 95.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 22.18 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.06 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.73→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 1.52 / Rsym value: 0.574 / % possible all: 72.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V7B Resolution: 1.73→32.23 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.479 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.103 / 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: 22.318 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→32.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.775 Å / Total num. of bins used: 20
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