+Open data
-Basic information
Entry | Database: PDB / ID: 2a1f | ||||||
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Title | Crystal Structure of Uridylate kinase | ||||||
Components | Uridylate kinase | ||||||
Keywords | TRANSFERASE / Uridylate kinase / PyrH / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Gorman, J. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Uridylate kinase Authors: Gorman, J. / Shapiro, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a1f.cif.gz | 285.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a1f.ent.gz | 232.9 KB | Display | PDB format |
PDBx/mmJSON format | 2a1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/2a1f ftp://data.pdbj.org/pub/pdb/validation_reports/a1/2a1f | HTTPS FTP |
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-Related structure data
Related structure data | 2bneS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Details | HomoHexamer, generated by chains A, B, C, D, E, F |
-Components
#1: Protein | Mass: 26971.270 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: pyrH, smbA / Plasmid: modified pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 References: UniProt: P43890, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor #2: 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: 2.99 Å3/Da / Density % sol: 58.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG4K, 0.1M Bis-Tris pH6.5, 0.6M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 2, 2003 |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 105743 / Num. obs: 105743 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 2.88 / Num. unique all: 9707 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2BNE Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.879 / SU B: 5.127 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.21 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.372 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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