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Yorodumi- PDB-4z38: Crystal structure of enoyl reductase domain of MlnA from the macr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z38 | ||||||
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Title | Crystal structure of enoyl reductase domain of MlnA from the macrolactin biosynthesis cluster from Bacillus amyloliquefaciens | ||||||
Components | MlnA | ||||||
Keywords | TRANSFERASE / polyketide / pks / enoyl reductase / trans-AT PKS / AT-less / TIM barrel | ||||||
Function / homology | Function and homology information [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid biosynthetic process / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus amyloliquefaciens subsp. plantarum | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Jakob, R.P. / Martin, S.F. / Herbst, D.A. / Maier, T. | ||||||
Citation | Journal: To Be Published Title: The structural organization of trans-AT polyketide synthases: ketoacyl synthase and trans-acting enoyl reductase Authors: Martin, S.F. / Jakob, R.P. / Herbst, D.A. / Maier, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z38.cif.gz | 514.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z38.ent.gz | 437.6 KB | Display | PDB format |
PDBx/mmJSON format | 4z38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z38_validation.pdf.gz | 974.6 KB | Display | wwPDB validaton report |
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Full document | 4z38_full_validation.pdf.gz | 982.5 KB | Display | |
Data in XML | 4z38_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 4z38_validation.cif.gz | 44.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/4z38 ftp://data.pdbj.org/pub/pdb/validation_reports/z3/4z38 | HTTPS FTP |
-Related structure data
Related structure data | 4z37C 2z6jS 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: 53072.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens subsp. plantarum (strain DSM 23117 / BGSC 10A6 / FZB42) (bacteria) Strain: DSM 23117 / BGSC 10A6 / FZB42 / Gene: mlnA, RBAM_014330 / Plasmid: pNIC28a-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL / References: UniProt: A7Z470 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15 % PEG3350, 0.2 M sodium malonate, pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→108.05 Å / Num. obs: 23587 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 95.35 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.8→2.92 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.7 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z6J Resolution: 2.8→108.05 Å / Cor.coef. Fo:Fc: 0.8982 / Cor.coef. Fo:Fc free: 0.8992 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.396
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Displacement parameters | Biso mean: 120.43 Å2
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Refine analyze | Luzzati coordinate error obs: 0.849 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→108.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.92 Å / Total num. of bins used: 12
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Refinement TLS params. | T12: 0.152 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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