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Yorodumi- PDB-2h92: Crystal Structure of Staphylococcus aureus Cytidine Monophosphate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h92 | ||||||
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Title | Crystal Structure of Staphylococcus aureus Cytidine Monophosphate Kinase in complex with cytidine-5'-monophosphate | ||||||
Components | Cytidylate kinase | ||||||
Keywords | TRANSFERASE / Rossmann fold | ||||||
Function / homology | Function and homology information (d)CMP kinase / (d)CMP kinase activity / pyrimidine nucleotide metabolic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Dhaliwal, B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Structure of Staphylococcus aureus cytidine monophosphate kinase in complex with cytidine 5'-monophosphate. Authors: Dhaliwal, B. / Ren, J. / Lockyer, M. / Charles, I. / Hawkins, A.R. / Stammers, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h92.cif.gz | 148.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h92.ent.gz | 116.7 KB | Display | PDB format |
PDBx/mmJSON format | 2h92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h92_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2h92_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2h92_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 2h92_validation.cif.gz | 43.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/2h92 ftp://data.pdbj.org/pub/pdb/validation_reports/h9/2h92 | HTTPS FTP |
-Related structure data
Related structure data | 1kdoS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 24628.996 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cmk / Plasmid: pET15b / Production host: Escherichia coli (E. coli) References: UniProt: Q1YBX2, UniProt: P63807*PLUS, UMP/CMP kinase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: 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: 3.71 Å3/Da / Density % sol: 66.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 1.6M ammonium sulfate, 0.1M Hepes, 2% PEG 200, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 5, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 48287 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6.9 % / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KDO Resolution: 2.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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Xplor file |
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