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- PDB-1y3h: Crystal Structure of Inorganic Polyphosphate/ATP-NAD kinase from ... -

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Basic information

Entry
Database: PDB / ID: 1y3h
TitleCrystal Structure of Inorganic Polyphosphate/ATP-NAD kinase from Mycobacterium tuberculosis
ComponentsInorganic polyphosphate/ATP-NAD kinase
KeywordsTRANSFERASE / NAD kinase / polyphosphate / NAD / ATP
Function / homology
Function and homology information


NAD+ kinase / polyphosphate metabolic process / NAD+ kinase activity / NADP biosynthetic process / NAD metabolic process / phosphorylation / NAD binding / 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 / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / 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 / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / Tumour Suppressor Smad4 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NAD kinase / NAD kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.8 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 24, 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: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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


Theoretical massNumber of molelcules
Total (without water)65,9112
Polymers65,9112
Non-polymers00
Water48627
1
A: Inorganic polyphosphate/ATP-NAD kinase
B: Inorganic polyphosphate/ATP-NAD kinase

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


Theoretical massNumber of molelcules
Total (without water)131,8234
Polymers131,8234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Unit cell
Length a, b, c (Å)140.176, 69.443, 106.433
Angle α, β, γ (deg.)90.00, 130.29, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a tetramer

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Components

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


Mass: 32955.711 Da / Num. of mol.: 2 / Mutation: T302I
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, Sodium 2-morpholinoethanesulfonic acid, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 4, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 34670 / Num. obs: 18419 / % possible obs: 91.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 51.5 Å2 / Rsym value: 0.063
Reflection shellResolution: 2.8→2.89 Å / % possible all: 78.39

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Processing

Software
NameVersionClassification
CNS1.1refinement
SADIEdata reduction
SAINTdata scaling
PHASESphasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→9.96 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1056320.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.235 716 4.8 %RANDOM
Rwork0.221 ---
obs0.235 15057 79.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.4984 Å2 / ksol: 0.312612 e/Å3
Displacement parametersBiso mean: 60.4 Å2
Baniso -1Baniso -2Baniso -3
1--13.63 Å20 Å23.52 Å2
2--16.48 Å20 Å2
3----2.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.8→9.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4043 0 0 27 4070
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.742.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 91 5.5 %
Rwork0.355 1575 -
obs--53.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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