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Yorodumi- PDB-3bzm: Crystal Structure of Open form of Menaquinone-Specific Isochorism... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bzm | ||||||
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Title | Crystal Structure of Open form of Menaquinone-Specific Isochorismate Synthase, MenF | ||||||
Components | Menaquinone-specific isochorismate synthase | ||||||
Keywords | ISOMERASE / chorismate / isochorismate / menaquinone / Menaquinone biosynthesis | ||||||
Function / homology | Function and homology information isochorismate synthase / isochorismate synthase activity / menaquinone biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Parsons, J.F. / Shi, K.M. / Ladner, J.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structure of isochorismate synthase in complex with magnesium. Authors: Parsons, J.F. / Shi, K.M. / Ladner, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bzm.cif.gz | 99.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bzm.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/3bzm ftp://data.pdbj.org/pub/pdb/validation_reports/bz/3bzm | HTTPS FTP |
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-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: 48823.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: menF, yfbA / Plasmid: Pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38051, isochorismate synthase |
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#2: Chemical | ChemComp-CIT / |
#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: 2.54 Å3/Da / Density % sol: 51.56 % |
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Crystal grow | Temperature: 298 K / Method: sitting drop vapor diffusion / pH: 8 Details: well solution: 0.2M sodium citrate, 6% glycerol, 8% PEG 3350, 5mM chorismic acid. protein solution: 50mM Tris, 5 mM magnesium chloride, 1 mM DTT, pH 7.6, 20 mg/mL. Drops were equal volumes ...Details: well solution: 0.2M sodium citrate, 6% glycerol, 8% PEG 3350, 5mM chorismic acid. protein solution: 50mM Tris, 5 mM magnesium chloride, 1 mM DTT, pH 7.6, 20 mg/mL. Drops were equal volumes well and protein., sitting drop vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 105 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: MSC Blue Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→19.67 Å / Num. obs: 36355 / % possible obs: 98.1 % / Redundancy: 7.97 % / Rmerge(I) obs: 0.064 / Χ2: 1 / Net I/σ(I): 14.7 / Scaling rejects: 2189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.67 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.357 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.543 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→19.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.054 Å / Total num. of bins used: 10
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