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- PDB-1y3i: Crystal Structure of Mycobacterium tuberculosis NAD kinase-NAD complex -

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Basic information

Entry
Database: PDB / ID: 1y3i
TitleCrystal Structure of Mycobacterium tuberculosis NAD kinase-NAD complex
ComponentsInorganic polyphosphate/ATP-NAD kinase
KeywordsTRANSFERASE / NAD kinase / polyphosphate / NAD / Mycobacterium tuberculosis
Function / homology
Function and homology information


polyphosphate metabolic process / NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / phosphorylation / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / Probable inorganic polyphosphate/atp-NAD kinase; domain 2 / ATP-NAD kinase C-terminal domain / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Tumour Suppressor Smad4 / Sandwich ...Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / Probable inorganic polyphosphate/atp-NAD kinase; domain 2 / ATP-NAD kinase C-terminal domain / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Tumour Suppressor Smad4 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD kinase / NAD kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMori, S. / Yamasaki, M. / Maruyama, Y. / Momma, K. / Kawai, S. / Hashimoto, W. / Mikami, B. / Murata, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2005
Title: NAD-binding mode and the significance of intersubunit contact revealed by the crystal structure of Mycobacterium tuberculosis NAD kinase-NAD complex
Authors: Mori, S. / Yamasaki, M. / Maruyama, Y. / Momma, K. / Kawai, S. / Hashimoto, W. / Mikami, B. / Murata, K.
History
DepositionNov 25, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inorganic polyphosphate/ATP-NAD kinase
B: Inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6799
Polymers65,8872
Non-polymers1,7917
Water77543
1
A: Inorganic polyphosphate/ATP-NAD kinase
B: Inorganic polyphosphate/ATP-NAD kinase
hetero molecules

A: Inorganic polyphosphate/ATP-NAD kinase
B: Inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,35718
Polymers131,7754
Non-polymers3,58314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area16960 Å2
ΔGint-116 kcal/mol
Surface area32600 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)110.450, 110.450, 108.932
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
DetailsThe biological unit is a tetramer generated from the dimer in the asymmetric unit by the operations: -x, -y, z.

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Components

#1: Protein Inorganic polyphosphate/ATP-NAD kinase / Poly(P)/ATP NAD kinase


Mass: 32943.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pPnk / Plasmid: pSK27 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P0A5S6, UniProt: P9WHV7*PLUS, NAD+ kinase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.79 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium sulfate, HEPES-Na, NAD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 22375 / % possible obs: 97.5 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 2.6→2.69 Å / % possible all: 86.8

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→10 Å / Num. parameters: 14548 / Num. restraintsaints: 19678 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.215 --RANDOM
all0.1911 ---
obs-21896 91 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3636
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3476 0 117 43 3636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.026
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0.058
X-RAY DIFFRACTIONs_from_restr_planes0.0264
X-RAY DIFFRACTIONs_zero_chiral_vol0.025
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.028
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.073
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.078
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 2.6→2.7 Å /
RfactorNum. reflection
Rwork0.313 -
obs-2222

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