+Open data
-Basic information
Entry | Database: PDB / ID: 4gdm | ||||||
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Title | Crystal Structure of E.coli MenH | ||||||
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 / MenH | ||||||
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: 2.75 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 | 4gdm.cif.gz | 157.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gdm.ent.gz | 125.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gdm_validation.pdf.gz | 471.8 KB | Display | wwPDB validaton report |
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Full document | 4gdm_full_validation.pdf.gz | 476.6 KB | Display | |
Data in XML | 4gdm_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 4gdm_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/4gdm ftp://data.pdbj.org/pub/pdb/validation_reports/gd/4gdm | HTTPS FTP |
-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
#1: Protein | Mass: 29515.348 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2263, JW2258, menH, 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 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 4.58 Å3/Da / Density % sol: 73.16 % |
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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: MX2 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.75→45.774 Å / Num. all: 43461 / Num. obs: 43437 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 17.5 % / Biso Wilson estimate: 69.92 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4266 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→45.77 Å / Cor.coef. Fo:Fc: 0.9414 / Cor.coef. Fo:Fc free: 0.9149 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.291 / SU Rfree Blow DPI: 0.225 / SU Rfree Cruickshank DPI: 0.228 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 135.83 Å2 / Biso mean: 53.7247 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.367 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→45.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.82 Å / Total num. of bins used: 20
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