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Yorodumi- PDB-4rvn: Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rvn | |||||||||
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Title | Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution | |||||||||
Components | Phenylacetate-coenzyme A ligase | |||||||||
Keywords | LIGASE / Acetyl-CoA synthetase-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | |||||||||
Function / homology | Function and homology information phenylacetate-CoA ligase / phenylacetate-CoA ligase activity / phenylacetate catabolic process / nucleotide binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | |||||||||
Authors | Joint Center for Structural Genomics (JCSG) | |||||||||
Citation | Journal: To be published Title: Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution Authors: Joint Center for Structural Genomics (JCSG) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rvn.cif.gz | 713.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rvn.ent.gz | 596 KB | Display | PDB format |
PDBx/mmJSON format | 4rvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/4rvn ftp://data.pdbj.org/pub/pdb/validation_reports/rv/4rvn | HTTPS FTP |
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-Related structure data
Related structure data | 4rvoS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 50203.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_0428 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8AAN6 |
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-Non-polymers , 8 types, 698 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-AMP / #4: Chemical | #5: Chemical | ChemComp-K / #6: Chemical | ChemComp-UNL / Num. of mol.: 4 / Source method: obtained synthetically #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-EDO / #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE CONSTRUCT (RESIDUES 1-435) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 1-435) WAS EXPRESSED WITH A PURIFICATI |
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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: 2.42 Å3/Da / Density % sol: 49.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 0.200M potassium sulfate, 20.00% polyethylene glycol 3350, No Buffer pH 6.7, 3mM AMP, 3mM CoA, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 22, 2010 / Details: double crystal monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91837 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→47.782 Å / Num. obs: 99670 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.127 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 12.85 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RVO Resolution: 2.2→47.782 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9301 / Occupancy max: 1 / Occupancy min: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. PROTEIN ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION. 4. THE MODELING OF ZINC IS SUPPORTED BY X-RAY FLUORESCENCE AND ANOMALOUS DIFFERENCE MAPS. 5. POTASSIUM (K) AND SULFATE (SO4) FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 1,2-ETHANEDIOL (EDO) USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE. 6. ADENOSINE-5'-MONOSPHATE (AMP), A CRYSTALLIZATION ADDITIVE, WAS MODELED INTO THE ACTIVE SITE ON ALL FOUR SUBUNITS IN THE ASYMMETRIC UNIT. HOWEVER, ADDITIONAL UNEXPLAINED ELECTRON DENSITIES AT THE ACTIVE SITE WERE MODELED AS UNKNOWN LIGANDS (UNL). 7. COENZYME A (COA), A CO-CRYSTALLIZATION ADDITIVE, WAS MODELED WITH PARTIAL OCCUPANCY INTO INTO SUBUNITS A AND C. HOWEVER, ELECTRON DENSITY FOR THE PANTOTHENATIC ACID MOIETIES WERE DISORDERED AND THIS PORTION OF THE COA MOLECULE COULD NOT BE RELIABLY MODELED
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Displacement parameters | Biso max: 161.26 Å2 / Biso mean: 57.5675 Å2 / Biso min: 21.59 Å2
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Refine analyze | Luzzati coordinate error obs: 0.347 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→47.782 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.26 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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