+Open data
-Basic information
Entry | Database: PDB / ID: 5dz6 | ||||||
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Title | Acyl transferase from Bacillaene PKS | ||||||
Components | Polyketide biosynthesis malonyl CoA-acyl carrier protein transacylase PksC | ||||||
Keywords | TRANSFERASE / polyketide synthase / acyltrasferase | ||||||
Function / homology | Function and homology information [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å | ||||||
Authors | Till, M. / Race, P.R. | ||||||
Citation | Journal: To Be Published Title: Architectural hierarchy of trans-acting enoyl reductases from polyunsaturated fatty acid and trans-acyltransferase polyketide synthases Authors: Till, M. / Burton, N.J. / Akrill, T.D. / van der Kamp, M.W. / Baker, G.E. / Byrne, M.J. / Owen, R.L. / Willis, C.L. / Race, P.R. #1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2011 Title: Crystallization and preliminary X-ray analysis of the bacillaene synthase trans-acting acyltransferase PksC. Authors: Cuskin, F. / Solovyova, A.S. / Lewis, R.J. / 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 | 5dz6.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dz6.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 5dz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dz6_validation.pdf.gz | 460.3 KB | Display | wwPDB validaton report |
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Full document | 5dz6_full_validation.pdf.gz | 463.2 KB | Display | |
Data in XML | 5dz6_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 5dz6_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/5dz6 ftp://data.pdbj.org/pub/pdb/validation_reports/dz/5dz6 | HTTPS FTP |
-Related structure data
Related structure data | 3g87S S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32448.025 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Gene: pksC, BSU17100 / Production host: Escherichia coli (E. coli) References: UniProt: O34825, [acyl-carrier-protein] S-malonyltransferase |
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-Non-polymers , 6 types, 310 molecules
#2: Chemical | ChemComp-GOL / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-PEG / | #7: 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: 2.2 Å3/Da / Density % sol: 44.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: PEG 3350, 0.2M sodium bromide, 0.1M bistris propane pH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9699 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9699 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→37.09 Å / Num. all: 71820 / Num. obs: 51033 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.44→1.51 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.067 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.306 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3g87 Resolution: 1.44→37.09 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.2009 / WRfactor Rwork: 0.1769 / FOM work R set: 0.9072 / SU B: 0.876 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0626 / SU Rfree: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 61.51 Å2 / Biso mean: 12.465 Å2 / Biso min: 2.8 Å2
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Refinement step | Cycle: final / Resolution: 1.44→37.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.436→1.473 Å / Total num. of bins used: 20
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