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Yorodumi- PDB-1t5h: 4-Chlorobenzoyl-CoA Ligase/Synthetase unliganded, selenomethionine -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t5h | ||||||
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Title | 4-Chlorobenzoyl-CoA Ligase/Synthetase unliganded, selenomethionine | ||||||
Components | 4-chlorobenzoyl CoA ligase | ||||||
Keywords | LIGASE / Adenylate-forming coenzyme A Ligase domain alternation conformational change | ||||||
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. AL3007 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.002 Å | ||||||
Authors | Gulick, A.M. / Lu, X. / Dunaway-Mariano, D. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Crystal Structure of 4-Chlorobenzoate:CoA Ligase/Synthetase in the Unliganded and Aryl Substrate-Bound States Authors: Gulick, A.M. / Lu, X. / 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 | 1t5h.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t5h.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 1t5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t5h_validation.pdf.gz | 424.7 KB | Display | wwPDB validaton report |
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Full document | 1t5h_full_validation.pdf.gz | 427.7 KB | Display | |
Data in XML | 1t5h_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 1t5h_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/1t5h ftp://data.pdbj.org/pub/pdb/validation_reports/t5/1t5h | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 54850.059 Da / Num. of mol.: 1 Mutation: SeMet1, SeMet7, SeMet102, SeMet185, SeMet203, SeMet284, SeMet310, SeMet315, SeMet324, SeMet404 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes sp. AL3007 (bacteria) / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q8GN86, EC: 6.2.1.33 |
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#2: Chemical | ChemComp-CA / |
#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: 2.84 Å3/Da / Density % sol: 56.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 6-8% PEG 4000; 10% glycerol; 0.25 M CaCl2; 50 mM CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.950038 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Jul 14, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.950038 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 41528 / Num. obs: 41528 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.516 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.002→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.794 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.44 Å2
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Refinement step | Cycle: LAST / Resolution: 2.002→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.002→2.053 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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