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- PDB-4anc: CRYSTAL FORM I OF THE D93N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINAS... -
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Open data
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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 | ||||||
![]() | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Georgescauld, F. / Moynie, L. / Habersetzer, J. / Lascu, I. / Dautant, A. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.1 KB | Display | ![]() |
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PDB format | ![]() | 48.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4andC ![]() 1k44S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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