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Yorodumi- PDB-6hp2: Crystal Structure of the O-Methyltransferase from the trans-AT PK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hp2 | ||||||
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Title | Crystal Structure of the O-Methyltransferase from the trans-AT PKS multienzyme C0ZGQ3 of Brevibacillus brevis in complex with S-Adenosyl-L-homocysteine | ||||||
Components | Putative polyketide synthase | ||||||
Keywords | TRANSFERASE / Polyketide / PKS / natural product / biosynthesis | ||||||
Function / homology | Function and homology information phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | Brevibacillus brevis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Jakob, R.P. / Felber, P. / Demyanenko, Y. / Delbart, F. / Maier, T. | ||||||
Citation | Journal: To Be Published Title: Structural and Functional Analysis of an O-Methyltransferase from the trans-AT PKS biosynthesis pathway Authors: Jakob, R. / Felber, P. / Demyanenko, Y. / Delbart, F. / Maier, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hp2.cif.gz | 195.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hp2.ent.gz | 156.1 KB | Display | PDB format |
PDBx/mmJSON format | 6hp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/6hp2 ftp://data.pdbj.org/pub/pdb/validation_reports/hp/6hp2 | HTTPS FTP |
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-Related structure data
Related structure data | 6hp1SC 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
#1: Protein | Mass: 39469.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevibacillus brevis (strain 47 / JCM 6285 / NBRC 100599) (bacteria) Gene: BBR47_39850 / Plasmid: pBX-NH3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0ZGQ3 |
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#2: Chemical | ChemComp-SAH / |
#3: 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: 2.38 Å3/Da / Density % sol: 48.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Na K Phosphate, 0.1M BisTrisPropane, 18.5% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.595 Å / Num. obs: 29127 / % possible obs: 99.62 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.037 / Rrim(I) all: 0.134 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.319 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2819 / CC1/2: 0.65 / Rpim(I) all: 0.464 / Rrim(I) all: 1.401 / % possible all: 96.44 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HP1 Resolution: 1.9→45.595 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→45.595 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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