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Yorodumi- PDB-1g3u: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g3u | ||||||
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Title | CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) | ||||||
Components | THYMIDYLATE KINASE | ||||||
Keywords | TRANSFERASE / TRANSFERASE (ATP:TMP PHOSPHOTRANSFERASE) / KINASE | ||||||
Function / homology | Function and homology information TMP metabolic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / GTP binding / magnesium ion binding / protein homodimerization activity ...TMP metabolic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å | ||||||
Authors | Li de la Sierra, I. / Munier-Lehmann, H. / Gilles, A.M. / Barzu, O. / Delarue, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: X-ray structure of TMP kinase from Mycobacterium tuberculosis complexed with TMP at 1.95 A resolution. Authors: Li de la Sierra, I. / Munier-Lehmann, H. / Gilles, A.M. / Barzu, O. / Delarue, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and preliminary X-ray analysis of the thymidylate kinase from Mycobacterium tuberculosis Authors: Li de la Sierra, I. / Munier-Lehmann, H. / Gilles, A.M. / Barzu, O. / Delarue, M. #2: Journal: To be Published Title: THYMIDYLATE KINASE OF MYCOBACTERIUM TUBERCULOSIS : A CHIMERA SHARING PROPERTIES COMMON TO EUKARYOTIC AND BACTERIALENZYMES Authors: Munier-Lehmann, H. / Chaffotte, A. / Labesse, G. / Pochet, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g3u.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g3u.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 1g3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/1g3u ftp://data.pdbj.org/pub/pdb/validation_reports/g3/1g3u | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a homodimer |
-Components
#1: Protein | Mass: 22662.525 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) References: UniProt: O05891, UniProt: P9WKE1*PLUS, dTMP kinase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-TMP / | #5: 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: 2.51 Å3/Da / Density % sol: 51.02 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 2000, ammonium sulfate, magnesium acetate, beta-mercaptoethanol, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.94 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 23, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→38.31 Å / Num. all: 17694 / Num. obs: 17694 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 38.1 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 8.6 / Num. unique all: 1209 / % possible all: 100 |
Reflection | *PLUS % possible obs: 100 % / Num. measured all: 184676 |
Reflection shell | *PLUS % possible obs: 99.9 % / Num. unique obs: 1209 |
-Processing
Software |
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Refinement | Resolution: 1.95→20 Å / σ(F): 0 / Stereochemistry target values: PROTEIN dict.
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.216 / Rfactor Rfree: 0.25 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |