+Open data
-Basic information
Entry | Database: PDB / ID: 4yxt | ||||||
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Title | PksG, a HMG-CoA Synthase from Bacillus subtilus | ||||||
Components | Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-ACP synthase PksG | ||||||
Keywords | TRANSFERASE / bacillaene / polyketide | ||||||
Function / homology | Function and homology information Transferases; Acyltransferases; Acyl groups converted into alkyl groups on transfer / hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / acetyl-CoA metabolic process / antibiotic biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Till, M. / Nair, A.V. / Robson, A. / Race, P.R. | ||||||
Citation | Journal: To Be Published Title: PksG, a HMG-CoA Synthase from Bacillus subtilus Authors: Till, M. / Nair, A.V. / Robson, A. / Race, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yxt.cif.gz | 167.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yxt.ent.gz | 132.4 KB | Display | PDB format |
PDBx/mmJSON format | 4yxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yxt_validation.pdf.gz | 438.7 KB | Display | wwPDB validaton report |
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Full document | 4yxt_full_validation.pdf.gz | 451.4 KB | Display | |
Data in XML | 4yxt_validation.xml.gz | 31 KB | Display | |
Data in CIF | 4yxt_validation.cif.gz | 43.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/4yxt ftp://data.pdbj.org/pub/pdb/validation_reports/yx/4yxt | 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
#1: Protein | Mass: 46771.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Gene: pksG, BSU17150 / Production host: Escherichia coli (E. coli) References: UniProt: P40830, Transferases; Acyltransferases; Acyl groups converted into alkyl groups on transfer #2: 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: 2.01 Å3/Da / Density % sol: 38.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: Morpheus screen A6 (molecular dimensions) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.9→64.7 Å / Num. obs: 60147 / % possible obs: 100 % / Redundancy: 10.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.232 / Rpim(I) all: 0.074 / Net I/σ(I): 7.4 / Num. measured all: 646983 / Scaling rejects: 171 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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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 / Resolution: 2.1→64.7 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2609 / WRfactor Rwork: 0.2032 / FOM work R set: 0.8279 / SU B: 5.916 / SU ML: 0.156 / SU R Cruickshank DPI: 0.2602 / SU Rfree: 0.2111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.211 / 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: 100.39 Å2 / Biso mean: 30.783 Å2 / Biso min: 12.65 Å2
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Refinement step | Cycle: final / Resolution: 2.1→64.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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