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Yorodumi- PDB-1kdt: CYTIDINE MONOPHOSPHATE KINASE FROM E.COLI IN COMPLEX WITH 2',3'-D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kdt | ||||||
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Title | CYTIDINE MONOPHOSPHATE KINASE FROM E.COLI IN COMPLEX WITH 2',3'-DIDEOXY-CYTIDINE MONOPHOSPHATE | ||||||
Components | CYTIDYLATE KINASE | ||||||
Keywords | TRANSFERASE / NUCLEOTIDE MONOPHOSPHATE KINASE | ||||||
Function / homology | Function and homology information (d)CMP kinase / CMP kinase activity / dCMP kinase activity / (d)CMP kinase activity / : / pyrimidine nucleotide metabolic process / nucleobase-containing small molecule interconversion / guanosine tetraphosphate binding / response to X-ray / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Bertrand, T. / Briozzo, P. / Assairi, L. / Ofiteru, A. / Bucurenci, N. / Munier-Lehmann, H. / Golinelli-Pimpaneau, B. / Barzu, O. / Gilles, A.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Sugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme. Authors: Bertrand, T. / Briozzo, P. / Assairi, L. / Ofiteru, A. / Bucurenci, N. / Munier-Lehmann, H. / Golinelli-Pimpaneau, B. / Barzu, O. / Gilles, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kdt.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kdt.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 1kdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kdt_validation.pdf.gz | 508.1 KB | Display | wwPDB validaton report |
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Full document | 1kdt_full_validation.pdf.gz | 501 KB | Display | |
Data in XML | 1kdt_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 1kdt_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/1kdt ftp://data.pdbj.org/pub/pdb/validation_reports/kd/1kdt | HTTPS FTP |
-Related structure data
Related structure data | 1kdoC 1kdpC 1kdrC 2cmkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24778.334 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cmk / Plasmid: pHSP210 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6I0, UMP/CMP kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.87 % | ||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: Ammonium Sulphate, TRIS-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 293K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||
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: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 22, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→35 Å / Num. all: 32964 / Num. obs: 30638 / % possible obs: 93 % / Observed criterion σ(I): 3 / Redundancy: 15.3 % / Rsym value: 7.3 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.95→2.02 Å / Mean I/σ(I) obs: 2.61 / Rsym value: 39.6 / % possible all: 96.1 |
Reflection | *PLUS Lowest resolution: 35 Å / Num. obs: 32964 / Num. measured all: 503844 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 96.1 % / Rmerge(I) obs: 0.396 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CMK Resolution: 1.95→35 Å / Isotropic thermal model: OVERALL ANISOTROPIC B / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: DISORDERED RESIDUES (A 1, A 2, A 226, A 227, B 1, B 2, B 226, B 227) AND DISORDERED SIDE-CHAINS (A 27, A 95, A 172, A 179, A 210, B 23, B 161) WERE NOT INCLUDED IN MODEL
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Displacement parameters | Biso mean: 34.7 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→35 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 35 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.221 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.7 Å2 |