+Open data
-Basic information
Entry | Database: PDB / ID: 4gec | ||||||
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Title | Crystal Structure of E.coli MenH R124A Mutant | ||||||
Components | 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase | ||||||
Keywords | LYASE / menaquinone biosynthesis / alpha beta hydrolase / 2-succinyl-6-hydroxy-2 / 4-cyclohexadiene-1-carboxylate synthase / mutant R124A / MenH mutant R124A | ||||||
Function / homology | Function and homology information 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase / 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase activity / menaquinone biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Johnston, J.M. / Baker, E.N. / Guo, Z. / Jiang, M. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Crystal Structures of E. coli Native MenH and Two Active Site Mutants. Authors: Johnston, J.M. / Jiang, M. / Guo, Z. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gec.cif.gz | 162.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gec.ent.gz | 128.2 KB | Display | PDB format |
PDBx/mmJSON format | 4gec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/4gec ftp://data.pdbj.org/pub/pdb/validation_reports/ge/4gec | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 29429.234 Da / Num. of mol.: 3 / Mutation: R124A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2263, JW2258, menH, MenH_R124Amutant, yfbB / Plasmid: pETM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P37355, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase |
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-Non-polymers , 5 types, 241 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: 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: 4.41 Å3/Da / Density % sol: 72.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Sodium Citrate, Ammonium sulfate, Lithium sulfate, pH 5.5, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953692 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 15, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.953692 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→117.444 Å / Num. all: 54795 / Num. obs: 54795 / % possible obs: 99.4 % / Redundancy: 14.9 % / Biso Wilson estimate: 61.48 Å2 / Rmerge(I) obs: 0.19 / Rsym value: 0.19 / Net I/σ(I): 17.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→81.42 Å / Cor.coef. Fo:Fc: 0.9363 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.223 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.187 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 141.12 Å2 / Biso mean: 49.133 Å2 / Biso min: 17.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.322 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→81.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Total num. of bins used: 20
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