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- PDB-1yt5: Crystal structure of NAD kinase from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1yt5
TitleCrystal structure of NAD kinase from Thermotoga maritima
Componentsinorganic polyphosphate/ATP-NAD kinase
KeywordsTRANSFERASE / domain 1: alpha/beta domain2: beta sandwich / Structural Genomics / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homology
Function and homology information


NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / 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
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsBerkeley Structural Genomics Center (BSGC)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Structure of a NAD kinase from Thermotoga maritima at 2.3 A resolution.
Authors: Oganesyan, V. / Huang, C. / Adams, P.D. / Jancarik, J. / Yokota, H.A. / Kim, R. / Kim, S.H.
History
DepositionFeb 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 14, 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
C: inorganic polyphosphate/ATP-NAD kinase
D: inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,85122
Polymers117,1224
Non-polymers1,72918
Water2,162120
1
A: inorganic polyphosphate/ATP-NAD kinase
D: inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,81015
Polymers58,5612
Non-polymers1,24913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-183 kcal/mol
Surface area23980 Å2
MethodPISA
2
B: inorganic polyphosphate/ATP-NAD kinase
C: inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0417
Polymers58,5612
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: inorganic polyphosphate/ATP-NAD kinase
D: inorganic polyphosphate/ATP-NAD kinase
hetero molecules

B: inorganic polyphosphate/ATP-NAD kinase
C: inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,85122
Polymers117,1224
Non-polymers1,72918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area14200 Å2
ΔGint-303 kcal/mol
Surface area40300 Å2
MethodPISA
4
A: inorganic polyphosphate/ATP-NAD kinase
D: inorganic polyphosphate/ATP-NAD kinase
hetero molecules

B: inorganic polyphosphate/ATP-NAD kinase
C: inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,85122
Polymers117,1224
Non-polymers1,72918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area9200 Å2
ΔGint-307 kcal/mol
Surface area45290 Å2
MethodPISA
5
A: inorganic polyphosphate/ATP-NAD kinase
hetero molecules

B: inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,42611
Polymers58,5612
Non-polymers8659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area4880 Å2
ΔGint-139 kcal/mol
Surface area22430 Å2
MethodPISA
6
D: inorganic polyphosphate/ATP-NAD kinase
hetero molecules

C: inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,42611
Polymers58,5612
Non-polymers8659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area4830 Å2
ΔGint-130 kcal/mol
Surface area22360 Å2
MethodPISA
7
A: inorganic polyphosphate/ATP-NAD kinase
hetero molecules

B: inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,42611
Polymers58,5612
Non-polymers8659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area2750 Å2
ΔGint-142 kcal/mol
Surface area24560 Å2
MethodPISA
8
D: inorganic polyphosphate/ATP-NAD kinase
hetero molecules

C: inorganic polyphosphate/ATP-NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,42611
Polymers58,5612
Non-polymers8659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area2630 Å2
ΔGint-133 kcal/mol
Surface area24560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.448, 137.153, 58.253
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsbilogical assembly is probably tetramer

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Components

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


Mass: 29280.578 Da / Num. of mol.: 4 / Fragment: NAD kinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: ppnK / Plasmid: pB4.1316B / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: Q9X255, NAD+ kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.24 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2004 / Details: monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→12 Å / Num. all: 44304 / Num. obs: 44304 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.08 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.358 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4827 / Rsym value: 0.33 / % possible all: 87

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHENIXmodel building
SOLVEphasing
REFMAC5refinement
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→12 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2361 -random
Rwork0.213 ---
all0.217 44304 --
obs0.217 44304 5.1 %-
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2--3.9 Å20 Å2
3----3.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.291 Å0.438 Å
Luzzati d res low-12 Å
Luzzati sigma a0.291 Å0.438 Å
Refinement stepCycle: LAST / Resolution: 2.3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8147 0 90 120 8357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_nbtor_refined7.2
X-RAY DIFFRACTIONr_angle_refined_deg1.539
X-RAY DIFFRACTIONr_gen_planes_refined0.006
X-RAY DIFFRACTIONr_bond_refined_d0.016
X-RAY DIFFRACTIONr_chiral_restr0.106
LS refinement shellResolution: 2.3→2.358 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.3 158 -
Rwork0.235 --
obs-3053 87 %

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