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Yorodumi- PDB-4ckw: Structure of the Mycobacterium tuberculosis Type II Dehydroquinas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ckw | ||||||
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Title | Structure of the Mycobacterium tuberculosis Type II Dehydroquinase N12S mutant (Crystal Form 1) | ||||||
Components | (3-DEHYDROQUINATE DEHYDRATASE) x 2 | ||||||
Keywords | LYASE / BACTERIAL PROTEINS / BINDING SITES / CRYSTALLIZATION / MODELS / MOLECULAR / MYCOBACTERIUM TUBERCULOSIS / TYPE 2 DEHYDROQUINASE / INHIBITOR / PROTEIN BINDING / PROTEIN STRUCTURE / SHIKIMIS ACID PATHWAY / SUBSTRATE SPECIFICITY | ||||||
Function / homology | Function and homology information quinate catabolic process / Chorismate via Shikimate Pathway / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Otero, J.M. / Llamas-Saiz, A.L. / Maneiro, M. / Peon, A. / Sedes, A. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J. | ||||||
Citation | Journal: To be Published Title: Investigation of the Dehydratation Mechanism Catalyzed by the Type II Dehydroquinase Authors: Maneiro, M. / Otero, J.M. / Peon, A. / Sedes, A. / Llamas-Saiz, A.L. / Lamb, H. / Hawkins, A.R. / van Raaij, M.J. / 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 | 4ckw.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ckw.ent.gz | 74.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ckw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/4ckw ftp://data.pdbj.org/pub/pdb/validation_reports/ck/4ckw | HTTPS FTP |
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-Related structure data
Related structure data | 4ckxC 4ckyC 4ckzC 4cl0C 4v0sC 2y71S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 15663.739 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): SK3430 References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase | ||||
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#2: Protein | Mass: 15649.712 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): SK3430 References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.4 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 12% GLYCEROL, 1.5 M AMMONIUM SULPHATE, 0.1 M TRIS-HCL PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97922 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 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: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→94.29 Å / Num. obs: 11546 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.6 / % possible all: 99.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y71 Resolution: 2.7→60.86 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.812 / SU B: 17.577 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R Free: 0.472 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GAP BY DISORDERED REGION BETWEEN SER-12 AND HIS-29, VAL- 105 AND SER-118 IN CHAIN A, SER-12 AND THR-27, ASN-104 AND SER-118 IN CHAIN B, SER- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GAP BY DISORDERED REGION BETWEEN SER-12 AND HIS-29, VAL- 105 AND SER-118 IN CHAIN A, SER-12 AND THR-27, ASN-104 AND SER-118 IN CHAIN B, SER-12 AND GLY-26, ASN-104 AND PRO-119 IN CHAIN C, LEU-13 AND TYR-24, GLY-78 AND THR-82, VAL-105 AND LEU- 117 IN CHAIN D.
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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: 36.218 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→60.86 Å
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