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Yorodumi- PDB-1nhk: CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nhk | ||||||
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Title | CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS RESOLUTION | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Keywords | PHOSPHOTRANSFERASE | ||||||
Function / homology | Function and homology information nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Myxococcus xanthus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Strelkov, S. / Williams, R.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: The 1.9 A crystal structure of a nucleoside diphosphate kinase complex with adenosine 3',5'-cyclic monophosphate: evidence for competitive inhibition. Authors: Strelkov, S.V. / Perisic, O. / Webb, P.A. / Williams, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nhk.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nhk.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nhk_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1nhk_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1nhk_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 1nhk_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/1nhk ftp://data.pdbj.org/pub/pdb/validation_reports/nh/1nhk | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.0008, -0.9883, 0.1525), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 L 2 - L 144 R 2 - R 144 0.230 | |
-Components
#1: Protein | Mass: 16025.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: CMP / Plasmid: PUC119 DERIVED / Production host: Escherichia coli (E. coli) / References: UniProt: P15266, nucleoside-diphosphate kinase #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | FOR EACH POLYPEPTIDE CHAIN THE SINGLE CAMP MOLECULE BOUND TO IT WAS MODELED WITH TWO ALTERNATIVE ...FOR EACH POLYPEPTID | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.73 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 26296 / % possible obs: 99.1 % / Observed criterion σ(I): 0 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 27 Å / Redundancy: 4.3 % / Num. measured all: 113713 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2 Å / Rmerge(I) obs: 0.206 |
-Processing
Software |
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Refinement | Resolution: 1.9→6 Å / σ(F): 0
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Displacement parameters | Biso mean: 21.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_dihedral_angle_deg / Dev ideal: 22.4 |