[English] 日本語
Yorodumi- PDB-4and: CRYSTAL FORM II OF THE D93N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4and | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL FORM II OF THE D93N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / nuclease activity / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphoprotein phosphatase activity / Prevention of phagosomal-lysosomal fusion ...purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / nuclease activity / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphoprotein phosphatase activity / Prevention of phagosomal-lysosomal fusion / symbiont-mediated suppression of host innate immune response / extracellular region / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.808 Å | ||||||
Authors | Georgescauld, F. / Moynie, L. / Habersetzer, J. / Lascu, I. / Dautant, A. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Intersubunit Ionic Interactions Stabilize the Nucleoside Diphosphate Kinase of Mycobacterium Tuberculosis. Authors: Georgescauld, F. / Moynie, L. / Habersetzer, J. / Cervoni, L. / Mocan, I. / Borza, T. / Harris, P. / Dautant, A. / Lascu, I. #1: Journal: Proteins / Year: 2002 Title: X-Ray Structure of Mycobacterium Tuberculosis Nucleoside Diphosphate Kinase. Authors: Chen, Y. / Morera, S. / Mocan, J. / Lascu, I. / Janin, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4and.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4and.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 4and.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4and_validation.pdf.gz | 417.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4and_full_validation.pdf.gz | 419.4 KB | Display | |
Data in XML | 4and_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 4and_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/4and ftp://data.pdbj.org/pub/pdb/validation_reports/an/4and | HTTPS FTP |
-Related structure data
Related structure data | 4ancC 1k44S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 14521.485 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL References: UniProt: P84284, UniProt: P9WJH7*PLUS, nucleoside-diphosphate kinase #2: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.4 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 Details: 2.0 M AMMONIUM SULFATE, 2% (V/V) PEG400, 0.1 M HEPES, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→26.3 Å / Num. obs: 10722 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 11 % / Biso Wilson estimate: 69.93 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 2.81→2.95 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.9 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K44 Resolution: 2.808→26.295 Å / SU ML: 0.37 / σ(F): 0.11 / Phase error: 26.99 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.715 Å2 / ksol: 0.312 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.83 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.808→26.295 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|