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Yorodumi- PDB-4cnp: Structure of the Salmonella typhi type I dehydroquinase inhibited... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cnp | ||||||
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Title | Structure of the Salmonella typhi type I dehydroquinase inhibited by a 3-epiquinic acid derivative | ||||||
Components | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
Keywords | LYASE / SHIKIMIS ACID PATHWAY | ||||||
Function / homology | Function and homology information 3,4-dihydroxybenzoate biosynthetic 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 | SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Otero, J.M. / Llamas-Saiz, A.L. / Maneiro, M. / Peon, A. / Lence, E. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J. | ||||||
Citation | Journal: To be Published Title: Mechanistic Insight Into the Reaction Catalyzed by Type I Dehydroquinase Authors: Maneiro, M. / Peon, A. / Lence, E. / Otero, J.M. / Llamas-Saiz, A.L. / van Raaij, M.J. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cnp.cif.gz | 244 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cnp.ent.gz | 196.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cnp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/4cnp ftp://data.pdbj.org/pub/pdb/validation_reports/cn/4cnp | HTTPS FTP |
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-Related structure data
Related structure data | 4cnnC 1qfeS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27680.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24670, 3-dehydroquinate dehydratase #2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-CL / | #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: 2.1 Å3/Da / Density % sol: 39.9 % / Description: NONE |
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Crystal grow | pH: 6.4 / Details: 30% PEG 4000, 0.1 M CITRATE-PHOSPHATE PH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.09723 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2013 / Details: PLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR) |
Radiation | Monochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.09723 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→84.35 Å / Num. obs: 156242 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 8.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.15→1.21 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.2 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QFE Resolution: 1.15→51.17 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.944 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INHIBITOR INCLUDED IN ENZYME ACTIVE SITE BY SOAKING OF APO- CRYSTALS IN INHIBITOR SOLUTION
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.232 Å2
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Refinement step | Cycle: LAST / Resolution: 1.15→51.17 Å
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Refine LS restraints |
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