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Yorodumi- PDB-3zop: Arg90Cit chorismate mutase of Bacillus subtilis at 1.6 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zop | |||||||||
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Title | Arg90Cit chorismate mutase of Bacillus subtilis at 1.6 A resolution | |||||||||
Components | CHORISMATE MUTASE AROH | |||||||||
Keywords | ISOMERASE / PSEUDO-ALPHA BETA-BARREL | |||||||||
Function / homology | Function and homology information chorismate metabolic process / chorismate mutase / chorismate mutase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm Similarity search - Function | |||||||||
Biological species | BACILLUS SUBTILIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | |||||||||
Authors | Burschowsky, D. / vanEerde, A. / Okvist, M. / Kienhofer, A. / Kast, P. / Hilvert, D. / Krengel, U. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Electrostatic Transition State Stabilization Rather Than Reactant Destabilization Provides the Chemical Basis for Efficient Chorismate Mutase Catalysis. Authors: Burschowsky, D. / Van Eerde, A. / Okvist, M. / Kienhofer, A. / Kast, P. / Hilvert, D. / Krengel, U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zop.cif.gz | 310.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zop.ent.gz | 257.2 KB | Display | PDB format |
PDBx/mmJSON format | 3zop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/3zop ftp://data.pdbj.org/pub/pdb/validation_reports/zo/3zop | HTTPS FTP |
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-Related structure data
Related structure data | 3zo8C 3zp4C 3zp7C 1dbfS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14521.919 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P19080, chorismate mutase #2: Water | ChemComp-HOH / | |
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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: 2.19 Å3/Da / Density % sol: 43.9 % / Description: NONE |
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Crystal grow | pH: 6 Details: 100 MM MMT BUFFER ---MALIC ACID, MES, TRIS, IN MOLAR RATIOS OF 1:2:2, RESPECTIVELY--- PH 6.0, 150 MM CALCIUM CHLORIDE, 25% W/V PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Mar 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→43.47 Å / Num. obs: 76808 / % possible obs: 88.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.61→1.71 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 7.2 / % possible all: 77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DBF Resolution: 1.61→41.58 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.61 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.945 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→41.58 Å
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Refine LS restraints |
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