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Yorodumi- PDB-1nlk: CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nlk | ||||||
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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(PO4 AS ACCEPTOR) | ||||||
Function / homology | Function and homology information nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Myxococcus xanthus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Williams, R.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Crystal structure of Myxococcus xanthus nucleoside diphosphate kinase and its interaction with a nucleotide substrate at 2.0 A resolution. Authors: Williams, R.L. / Oren, D.A. / Munoz-Dorado, J. / Inouye, S. / Inouye, M. / Arnold, E. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Nucleoside Authors: Willaims, R.L. / Munoz-Dorado, J. / Jacobo-Molina, A. / Inouye, S. / Inouye, M. / Arnold, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nlk.cif.gz | 68.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nlk.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nlk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nlk_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1nlk_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1nlk_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 1nlk_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/1nlk ftp://data.pdbj.org/pub/pdb/validation_reports/nl/1nlk | HTTPS FTP |
-Related 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.0047, -0.9876, 0.157), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN L WHEN APPLIED TO CHAIN R. | |
-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) / References: UniProt: P15266, nucleoside-diphosphate kinase #2: Chemical | #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.94 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.2 / 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 | *PLUS Highest resolution: 2 Å / Num. obs: 21660 / Rmerge(I) obs: 0.072 |
-Processing
Software |
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Refinement | Resolution: 2→6 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 21660 / Rfactor all: 0.23 / Rfactor Rwork: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.69 |