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Yorodumi- PDB-4anc: CRYSTAL FORM I OF THE D93N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4anc | ||||||
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Title | CRYSTAL FORM I OF THE D93N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASENucleoside-diphosphate kinase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host innate immune response / : / 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 ...symbiont-mediated suppression of host innate immune response / : / 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 / protein autophosphorylation / extracellular region / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4anc.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4anc.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 4anc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/4anc ftp://data.pdbj.org/pub/pdb/validation_reports/an/4anc | HTTPS FTP |
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-Related structure data
Related structure data | 4andC 1k44S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14521.485 Da / Num. of mol.: 1 / 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 |
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#2: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.5 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 2.0 M AMMONIUM SULFATE, 0.1 M TRIS-HCL, PH 8.5 |
-Data collection
Diffraction | Mean temperature: 107 K |
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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: 2.8→26.9 Å / Num. obs: 6145 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 20.5 % / Biso Wilson estimate: 58.24 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 21 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 7.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K44 Resolution: 2.8→26.844 Å / SU ML: 0.36 / σ(F): 1.43 / Phase error: 24.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.685 Å2 / ksol: 0.323 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→26.844 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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