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Yorodumi- PDB-6x7q: Chloramphenicol acetyltransferase type III in complex with chlora... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x7q | |||||||||
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Title | Chloramphenicol acetyltransferase type III in complex with chloramphenicol and acetyl-oxa(dethia)-CoA | |||||||||
Components | Chloramphenicol acetyltransferase 3 | |||||||||
Keywords | TRANSFERASE / Chloramphenicol acetyltransferase / Antibiotic resistance | |||||||||
Function / homology | Function and homology information chloramphenicol O-acetyltransferase activity / chloramphenicol O-acetyltransferase / response to antibiotic Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | |||||||||
Authors | Benjamin, A.B. / Stunkard, L.M. / Ling, J. / Nice, J.N. / Lohman, J.R. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2023 Title: Structures of chloramphenicol acetyltransferase III and Escherichia coli beta-keto-acylsynthase III co-crystallized with partially hydrolysed acetyl-oxa(de-thia)CoA Authors: Benjamin, A.B. / Stunkard, L.M. / Ling, J. / Nice, J.N. / Lohman, J.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x7q.cif.gz | 174.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x7q.ent.gz | 136.1 KB | Display | PDB format |
PDBx/mmJSON format | 6x7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x7q_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 6x7q_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 6x7q_validation.xml.gz | 37.3 KB | Display | |
Data in CIF | 6x7q_validation.cif.gz | 54.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/6x7q ftp://data.pdbj.org/pub/pdb/validation_reports/x7/6x7q | HTTPS FTP |
-Related structure data
Related structure data | 6x7rC 3claS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 25091.480 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cat3 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P00484, chloramphenicol O-acetyltransferase |
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-Non-polymers , 6 types, 816 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.41 Å3/Da / Density % sol: 49.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM magnesium chloride, 100 mM sodium citrate:citric acid, pH 5.5, 46% PEG400 Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 5, 2019 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50 Å / Num. obs: 84122 / % possible obs: 100 % / Redundancy: 14.5 % / Biso Wilson estimate: 20.371 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.04 / Rrim(I) all: 0.152 / Rsym value: 0.092 / Χ2: 1.047 / Net I/av σ(I): 19.583 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1.261 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8292 / CC1/2: 0.813 / CC star: 0.947 / Rpim(I) all: 0.343 / Rrim(I) all: 1.308 / Rsym value: 1.231 / Χ2: 1.001 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3CLA Resolution: 1.68→34.33 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.192 / WRfactor Rwork: 0.1508 / FOM work R set: 0.8509 / SU B: 2.217 / SU ML: 0.071 / SU R Cruickshank DPI: 0.0945 / SU Rfree: 0.0981 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.098 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.15 Å2 / Biso mean: 18.716 Å2 / Biso min: 8.69 Å2
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Refinement step | Cycle: final / Resolution: 1.68→34.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.722 Å / Rfactor Rfree error: 0
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