+Open data
-Basic information
Entry | Database: PDB / ID: 2c4v | ||||||
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Title | H. pylori type II DHQase in complex with citrate | ||||||
Components | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
Keywords | LYASE / 3-DEHYDROQUINASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS | ||||||
Function / homology | Function and homology information quinate catabolic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process Similarity search - Function | ||||||
Biological species | HELICOBACTER PYLORI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å | ||||||
Authors | Robinson, D.A. / Lapthorn, A.J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2006 Title: Crystal Structures of Helicobacter Pylori Type II Dehydroquinase Inhibitor Complexes: New Directions for Inhibitor Design. Authors: Robinson, D.A. / Stewart, K.A. / Price, N.C. / Chalk, P.A. / Coggins, J.R. / Lapthorn, A.J. #1: Journal: Proteins: Struct.,Funct., Genet. / Year: 2003 Title: Crystal Structure of the Type II 3-Dehydroquinase from Helicobacter Pylori Authors: Lee, B.I. / Kwak, J.E. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c4v.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c4v.ent.gz | 32.7 KB | Display | PDB format |
PDBx/mmJSON format | 2c4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c4v_validation.pdf.gz | 386.6 KB | Display | wwPDB validaton report |
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Full document | 2c4v_full_validation.pdf.gz | 388.4 KB | Display | |
Data in XML | 2c4v_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 2c4v_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/2c4v ftp://data.pdbj.org/pub/pdb/validation_reports/c4/2c4v | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18499.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q48255, 3-dehydroquinate dehydratase |
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#2: Chemical | ChemComp-CIT / |
#3: Water | ChemComp-HOH / |
Compound details | CATALYZES A TRANS-DEHYDRATIO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.1 % Description: DATA USED WAS THAT OF ENTRY 1J2Y NO SIGMA CUTOFF WAS USED AND ALL DATA TO 2.5A RESOLUTION WAS USED |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG 4000, SODIUM CHOLRIDE, SODIUM CITRATE, EDTA, 2-MERCAPTOETHANOL, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→44 Å / Num. obs: 6146 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 38 % / Biso Wilson estimate: 53.5 Å2 / Rmerge(I) obs: 0.09 |
Reflection shell | Resolution: 2.5→2.64 Å / Rmerge(I) obs: 0.48 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 15.034 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.633 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY IS A REINTERPRETATION OF ENTRY 1J2Y USING DEPOSITED STRUCTURE FACTORS.
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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: 38.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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