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- PDB-1k44: Mycobacterium tuberculosis Nucleoside Diphosphate Kinase -

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Basic information

Entry
Database: PDB / ID: 1k44
TitleMycobacterium tuberculosis Nucleoside Diphosphate Kinase
ComponentsNucleoside Diphosphate Kinase
KeywordsTRANSFERASE / Nucleoside Triphosphate / Nucleoside Diphosphate
Function / homology
Function and homology information


symbiont-mediated perturbation of host Rab small GTPase signal transduction / purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / symbiont-mediated killing of host cell / nuclease activity / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process ...symbiont-mediated perturbation of host Rab small GTPase signal transduction / purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / symbiont-mediated killing of host cell / nuclease activity / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / 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
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside diphosphate kinase / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, Y. / Morera, S. / Lascu, I. / Janin, J.
Citation
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.
#1: Journal: Structure / Year: 1995
Title: Nucleoside Diphosphate Kinase B Complexed with GDP at 2 A Resolution
Authors: Morera, S. / Lacombe, M.L. / Xu, Y. / LeBras, G. / Janin, J.
History
DepositionOct 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside Diphosphate Kinase
B: Nucleoside Diphosphate Kinase
C: Nucleoside Diphosphate Kinase
D: Nucleoside Diphosphate Kinase
E: Nucleoside Diphosphate Kinase
F: Nucleoside Diphosphate Kinase


Theoretical massNumber of molelcules
Total (without water)87,1356
Polymers87,1356
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10470 Å2
ΔGint-28 kcal/mol
Surface area32450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.033, 98.818, 127.52
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nucleoside Diphosphate Kinase / E.C.2.7.4.6 / NDK / NDP kinase / Nucleoside-2-P kinase


Mass: 14522.470 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P84284, UniProt: P9WJH7*PLUS, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG4000, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
320 mM1dropMgCl2
4100 mMsodium citrate1drop
520 %iso-propanol1drop
620 %PEG40001drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2001
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 30399 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.137 / Net I/σ(I): 11.7
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2978 / Rsym value: 0.46 / % possible all: 97.5
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 99.5 % / Redundancy: 5.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.246 1512 random
Rwork0.205 --
all-30399 -
obs-30399 -
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6096 0 0 107 6203
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.4
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.205 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4

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