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Yorodumi- PDB-6x7r: E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x7r | |||||||||
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Title | E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) in complex with oxa(dethia)-coenzyme A | |||||||||
Components | 3-oxoacyl-[acyl-carrier-protein] synthase 3 | |||||||||
Keywords | TRANSFERASE / Ketoacyl synthase / substrate analog | |||||||||
Function / homology | Function and homology information beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid metabolic process / fatty acid biosynthetic process / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli str. K-12 substr. DH10B (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å | |||||||||
Authors | Benjamin, A.B. / Stunkard, L.M. / Ling, J. / Nice, J.N. / Lohman, J.R. | |||||||||
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 | 6x7r.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x7r.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 6x7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x7r_validation.pdf.gz | 697.6 KB | Display | wwPDB validaton report |
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Full document | 6x7r_full_validation.pdf.gz | 698.3 KB | Display | |
Data in XML | 6x7r_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 6x7r_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/6x7r ftp://data.pdbj.org/pub/pdb/validation_reports/x7/6x7r | HTTPS FTP |
-Related structure data
Related structure data | 6x7qC 1hnjS 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
#1: Protein | Mass: 33748.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K-12 substr. DH10B (bacteria) Strain: K12 / Gene: fabH, b1091, JW1077 / Variant: DH10B / Plasmid: pRSF / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0A6R0, beta-ketoacyl-[acyl-carrier-protein] synthase III |
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#2: Chemical | ChemComp-UT7 / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-DMS / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 75 mM magnesium chloride, 100 mM HEPES:NaOH, pH 7.5, 23% PEG3350, 1.5% DMSO 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: Jun 29, 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: 1.35→50 Å / Num. obs: 60608 / % possible obs: 99 % / Redundancy: 13.9 % / Biso Wilson estimate: 20.81 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.024 / Rrim(I) all: 0.089 / Rsym value: 0.071 / Χ2: 1.016 / Net I/av σ(I): 25.077 / Net I/σ(I): 130.4 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 6013 / CC1/2: 0.936 / CC star: 0.983 / Rpim(I) all: 0.211 / Rrim(I) all: 0.797 / Rsym value: 0.644 / Χ2: 1.034 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1HNJ Resolution: 1.35→23.59 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.1961 / WRfactor Rwork: 0.1604 / FOM work R set: 0.8552 / SU B: 0.976 / SU ML: 0.039 / SU R Cruickshank DPI: 0.05 / SU Rfree: 0.0543 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.054 / 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: 68.29 Å2 / Biso mean: 20.81 Å2 / Biso min: 14.81 Å2
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Refinement step | Cycle: final / Resolution: 1.35→23.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.383 Å / Rfactor Rfree error: 0
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