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- PDB-1n5k: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINAS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n5k | ||||||
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Title | CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE CRYSTALLIZED IN SODIUM MALONATE (RESOLUTION 2.1 A) | ||||||
![]() | THYMIDYLATE KINASE | ||||||
![]() | TRANSFERASE / TRANSFERASE (ATP:TMP PHOSPHOTRANSFERASE) / KINASE | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fioravanti, E. / Haouz, A. / Ursby, T. / Munier-Lehmann, H. / Delarue, M. / Bourgeois, D. | ||||||
![]() | ![]() Title: Mycobacterium tuberculosis Thymidylate Kinase: Structural Studies of Intermediates along the Reaction Pathway Authors: Fioravanti, E. / Haouz, A. / Ursby, T. / Munier-Lehmann, H. / Delarue, M. / Bourgeois, D. #1: ![]() Title: Cryo-Photolysis 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. #2: ![]() 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. #3: ![]() 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. | ||||||
History |
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Remark 600 | HETEROGEN HOH molecules 140 and 141 were both named 140 in the paper because they occupy the same ...HETEROGEN HOH molecules 140 and 141 were both named 140 in the paper because they occupy the same site in the 2 monomers (A and B), in order to make an easier comparison of the active sites. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.4 KB | Display | ![]() |
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PDB format | ![]() | 70.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n5iC ![]() 1n5jC ![]() 1n5lC ![]() 1gsiS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The asymmetric unit contains the functional dimer. |
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Components
#1: Protein | Mass: 22662.525 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O05891, UniProt: P9WKE1*PLUS, dTMP kinase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.4 M sodium malonate, 2% PEG 2000, 0.1 M MES pH 6.0, 2 mM b-mercaptoethanol, 25 mM magnesium acetate, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2001 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.936 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→19.73 Å / Num. all: 27942 / Num. obs: 27942 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 33.6 Å2 / Rsym value: 0.087 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4064 / Rsym value: 0.297 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GSI Resolution: 2.1→19.71 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1897368.07 / Data cutoff high rms absF: 1897368.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Monomer A contains the TMP complex. Monomer B contains the TMP-Mg++ complex.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.2277 Å2 / ksol: 0.351894 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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