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- PDB-4ckz: Structure of the Mycobacterium tuberculosis Type II Dehydroquinas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ckz | ||||||
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Title | Structure of the Mycobacterium tuberculosis Type II Dehydroquinase D88N mutant | ||||||
![]() | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
![]() | LYASE / BACTERIAL PROTEINS / TYPE 2 DEHYDROQUINASE / INHIBITOR / PROTEIN BINDING / PROTEIN STRUCTURE / SHIKIMIS ACID PATHWAY / SUBSTRATE SPECIFICITY | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.9 KB | Display | ![]() |
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PDB format | ![]() | 44 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 434.6 KB | Display | ![]() |
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Full document | ![]() | 437.7 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ckwC ![]() 4ckxC ![]() 4ckyC ![]() 4cl0C ![]() 4v0sC ![]() 2y71S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15675.753 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40.7 % / Description: NONE |
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Crystal grow | pH: 5.4 / Details: 32% PEG 4000, 0.1 M NA CITRATE PH 5.4 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
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 twin |
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Reflection | Resolution: 2.51→44 Å / Num. obs: 6028 / % possible obs: 80.7 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 51.8 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 13.3 | |||||||||||||||
Reflection shell | Resolution: 2.51→2.65 Å / Redundancy: 8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 6.4 / % possible all: 20.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y71 Resolution: 2.52→44 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.722 / SU B: 16.307 / SU ML: 0.351 / Cross valid method: THROUGHOUT / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY GAP BY DISORDERED REGION BETWEEN LEU-16 AND GLY-26, ARG- 108 AND SER-115 IN CHAIN A, GLY-17 AND TYR-24, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY GAP BY DISORDERED REGION BETWEEN LEU-16 AND GLY-26, ARG- 108 AND SER-115 IN CHAIN A, GLY-17 AND TYR-24, HIS-106 AND ARG-112 IN CHAIN B.
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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: 33.032 Å2
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Refinement step | Cycle: LAST / Resolution: 2.52→44 Å
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Refine LS restraints |
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