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Yorodumi- PDB-7cb3: Crystal structure of type III polyketide synthase from Mycobacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cb3 | ||||||
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Title | Crystal structure of type III polyketide synthase from Mycobacterium marinum | ||||||
Components | Chalcone/stilbene synthase | ||||||
Keywords | TRANSFERASE / Bacterial / TypeIII polyketide synthase | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | Mycobacterium marinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Pratap, S. / Kant, A. / Saxena, P. / Krishnan, V. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of type III polyketide synthase from Mycobacterium marinum. Authors: Pratap, S. / Kant, A. / Saxena, P. / Krishnan, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cb3.cif.gz | 282.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cb3.ent.gz | 228.5 KB | Display | PDB format |
PDBx/mmJSON format | 7cb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cb3_validation.pdf.gz | 748.4 KB | Display | wwPDB validaton report |
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Full document | 7cb3_full_validation.pdf.gz | 752.8 KB | Display | |
Data in XML | 7cb3_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 7cb3_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/7cb3 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/7cb3 | HTTPS FTP |
-Related structure data
Related structure data | 1tedS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 30 - 392 / Label seq-ID: 30 - 392
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-Components
#1: Protein | Mass: 44633.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria) Strain: ATCC BAA-535 / M / Gene: MMAR_2190 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2HNE1 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | 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: 3.48 Å3/Da / Density % sol: 64.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% (w/v) Polyethylene glycol 3000 and 100 mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.306→72.287 Å / Num. obs: 28212 / % possible obs: 90.4 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.027 / Rrim(I) all: 0.064 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.306→2.487 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1411 / CC1/2: 0.576 / Rpim(I) all: 0.487 / Rrim(I) all: 0.747 / % possible all: 68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TED Resolution: 2.31→72.287 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.936 / SU B: 17.221 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.594 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.669 Å2
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Refinement step | Cycle: 1 / Resolution: 2.31→72.287 Å
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Refine LS restraints |
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