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Yorodumi- PDB-2iyv: Shikimate kinase from Mycobacterium tuberculosis in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iyv | ||||||
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Title | Shikimate kinase from Mycobacterium tuberculosis in complex with ADP, open LID (conf. B) | ||||||
Components | SHIKIMATE KINASE | ||||||
Keywords | TRANSFERASE / AROMATIC AMINO ACID BIOSYNTHESIS / P-LOOP KINASE / METAL- BINDING / SHIKIMATE KINASE / SHIKIMATE PATHWAY / NUCLEOTIDE- BINDING / AMINO-ACID BIOSYNTHESIS / KINASE / MAGNESIUM / ATP-BINDING | ||||||
Function / homology | Function and homology information shikimate kinase / shikimate kinase activity / shikimate metabolic process / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Hartmann, M.D. / Bourenkov, G.P. / Oberschall, A. / Strizhov, N. / Bartunik, H.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Mechanism of Phosphoryl Transfer Catalyzed by Shikimate Kinase from Mycobacterium Tuberculosis. Authors: Hartmann, M.D. / Bourenkov, G.P. / Oberschall, A. / Strizhov, N. / Bartunik, H.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iyv.cif.gz | 89.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iyv.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 2iyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iyv_validation.pdf.gz | 769.7 KB | Display | wwPDB validaton report |
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Full document | 2iyv_full_validation.pdf.gz | 771.1 KB | Display | |
Data in XML | 2iyv_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 2iyv_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/2iyv ftp://data.pdbj.org/pub/pdb/validation_reports/iy/2iyv | HTTPS FTP |
-Related structure data
Related structure data | 2iyqSC 2iyrC 2iysC 2iytC 2iyuC 2iywC 2iyxC 2iyyC 2iyzC S: Starting model for refinement C: citing same article (ref.) |
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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: 19683.506 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P0A4Z2, UniProt: P9WPY3*PLUS, shikimate kinase |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Sequence details | C-TERMINAL HIS-TAG |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37.9 % |
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Crystal grow | pH: 6.5 / Details: 25%(W/V) PEG 3000, 100MM MES PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 12, 2001 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→19.28 Å / Num. obs: 34977 / % possible obs: 97.2 % / Redundancy: 2.51 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.35 |
Reflection shell | Resolution: 1.35→1.38 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.64 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IYQ Resolution: 1.35→19.28 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.154 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 14.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→19.28 Å
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Refine LS restraints |
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