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Yorodumi- PDB-1gsi: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gsi | ||||||
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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 / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding ...TMP metabolic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.6 Å | ||||||
Authors | Ursby, T. / Weik, M. / Fioravanti, E. / Delarue, M. / Goeldner, M. / Bourgeois, D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Cryophotolysis of Caged Compounds: A Technique for Trapping Intermediate States in Protein Crystals Authors: Ursby, T. / Weik, M. / Fioravanti, E. / Delarue, M. / Goeldner, M. / Bourgeois, D. #1: 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: De La Sierra Li, I. / Munier-Lehmann, H. / Gilles, A.M. / Barzu, O. / Delarue, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and Preliminary X-Ray Analysis of the Thymidylate Kinase from Mycobacterium Tuberculosis Authors: De La Sierra Li, I. / Munier-Lehmann, H. / Gilles, A.M. / Barzu, O. / Delarue, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gsi.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gsi.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 1gsi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/1gsi ftp://data.pdbj.org/pub/pdb/validation_reports/gs/1gsi | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 272 molecules
#2: Chemical | ChemComp-MG / | ||||
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#3: Chemical | ChemComp-TMP / | ||||
#4: Chemical | #5: Chemical | #6: 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: 2.5 Å3/Da / Density % sol: 50 % / Description: STARTING MODEL PDB ENTRY 1G3U | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: PROTEIN CRYSTALLIZED IN 1.4M AMMONIUM SULFATE, 100MM MES PH6, 2% PEG 2000, 25MM MAGNESIUM ACETATE 2MM BETA-MERCAPTOETHANOL, pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 7.4 / Method: vapor diffusion, hanging dropDetails: Li de La Sierra, I., (2000) Acta Crystallogr.,Sect., D56, 226. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.75 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 18, 2000 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.75 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25.2 Å / Num. obs: 30736 / % possible obs: 99.1 % / Redundancy: 8.2 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.076 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.282 / % possible all: 99.1 |
Reflection | *PLUS Num. measured all: 252502 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 98.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.282 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.6→25.19 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.3241 Å2 / ksol: 0.362529 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→25.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.231 |