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Yorodumi- PDB-2j4k: Crystal structure of uridylate kinase from Sulfolobus solfataricu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j4k | ||||||
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Title | Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UMP to 2.2 Angstrom resolution | ||||||
Components | URIDYLATE KINASE | ||||||
Keywords | TRANSFERASE / ASPARTOKINASE FAMILY / PYRIMIDINE BIOSYNTHESIS / KINASE / UMP KINASE / NUCLEOSIDE MONOPHOSPHATE KINASE / PYRIMIDINE NUCLEOTIDE SYNTHESIS | ||||||
Function / homology | Function and homology information UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Jensen, K.S. / Johansson, E. / Jensen, K.F. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Structural and Enzymatic Investigation of the Sulfolobus Solfataricus Uridylate Kinase Shows Competitive Utp Inhibition and the Lack of GTP Stimulation Authors: Jensen, K.S. / Johansson, E. / Jensen, K.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j4k.cif.gz | 264 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j4k.ent.gz | 213.5 KB | Display | PDB format |
PDBx/mmJSON format | 2j4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j4k_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 2j4k_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 2j4k_validation.xml.gz | 55.8 KB | Display | |
Data in CIF | 2j4k_validation.cif.gz | 73.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/2j4k ftp://data.pdbj.org/pub/pdb/validation_reports/j4/2j4k | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 25016.873 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-227 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q97ZE2, UMP kinase #2: Chemical | ChemComp-U5P / #3: Chemical | ChemComp-CD / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Sequence details | THE CRYSTALLIZED ENZYME WAS PREPARED WITH ONLY ONE MET RESIDUE IN THE N-TERMINAL, IN CONTRAST TO ...THE CRYSTALLIZ | |
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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: 2.41 Å3/Da / Density % sol: 46.1 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: PROTEIN SOLUTION (2UL) IN 10 MM TRIS/CL PH 7.6 WITH 4.6 MG/ML SSUMPK AND 2 MM UMP AND 5 MM MGCL2 MIXED WITH 2 UL MOTHER SOLUTION. MOTHER SOLUTION: 0.65 M SODIUM ACETATE, 100 MM CDCL2, 0.1 M ...Details: PROTEIN SOLUTION (2UL) IN 10 MM TRIS/CL PH 7.6 WITH 4.6 MG/ML SSUMPK AND 2 MM UMP AND 5 MM MGCL2 MIXED WITH 2 UL MOTHER SOLUTION. MOTHER SOLUTION: 0.65 M SODIUM ACETATE, 100 MM CDCL2, 0.1 M HEPES, PH 7.5. HANGING DROP VAPOR DIFFUSION TECHNIQUE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.008 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 30, 2005 / Details: VERTICALLY FOCUSING CYLINDRICAL MIRROR |
Radiation | Monochromator: SINGLE ASYMMETRICALLY CUT SI(111) CRYSTAL WITH HORIZONTAL DIFFRACTION PLANE Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→22.54 Å / Num. obs: 72006 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.3 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: URIDYLATE KINASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH UMP AND AMPPCP - HEXAMER - WITHOUT LIGANDS Resolution: 2.2→21.67 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2035549.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.1799 Å2 / ksol: 0.39084 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→21.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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