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- PDB-3pfn: Crystal Structure of human NAD kinase -

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Basic information

Entry
Database: PDB / ID: 3pfn
TitleCrystal Structure of human NAD kinase
ComponentsNAD kinase
KeywordsTRANSFERASE / Structural Genomics Consortium / SNP / SGC
Function / homology
Function and homology information


NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / Nicotinate metabolism / NAD metabolic process / positive regulation of insulin secretion involved in cellular response to glucose stimulus / ATP metabolic process / phosphorylation / ATP binding / metal ion binding / cytosol
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsWang, H. / Tempel, W. / Wernimont, A.K. / Tong, Y. / Guan, X. / Shen, Y. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Wang, H. / Tempel, W. / Wernimont, A.K. / Tong, Y. / Guan, X. / Shen, Y. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal Structure of human NAD kinase
Authors: Wang, H. / Tempel, W. / Wernimont, A.K. / Tong, Y. / Guan, X. / Shen, Y. / Li, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H.
History
DepositionOct 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD kinase
B: NAD kinase
C: NAD kinase
D: NAD kinase


Theoretical massNumber of molelcules
Total (without water)162,48066
Polymers162,4804
Non-polymers062
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13990 Å2
ΔGint-108 kcal/mol
Surface area49260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.095, 133.587, 162.668
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40619.922 Da / Num. of mol.: 4 / Fragment: UNP Residues 68-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NADK / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: O95544, NAD+ kinase
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 62 / Source method: obtained synthetically

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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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 21.4% PEG3350, 0.2M magnesium nitrate, pH 5.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 39854 / % possible obs: 98.4 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.115 / Χ2: 1.748 / Net I/σ(I): 24
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.7-2.88.30.8652.939491.09399.2
2.8-2.918.30.61439621.10899.1
2.91-3.048.30.44739701.05899.3
3.04-3.28.30.30239491.06498.9
3.2-3.48.30.19739601.10898.8
3.4-3.668.30.13439781.24798.7
3.66-4.038.20.10339511.63598.3
4.03-4.618.10.07639912.21498
4.61-5.880.06540122.43497.5
5.8-307.90.06441324.57195.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DMphasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.7→29.84 Å / Cor.coef. Fo:Fc: 0.9206 / Cor.coef. Fo:Fc free: 0.9077 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
Details: autosharp, buccaneer, resolve, refmac, phenix, coot, molprobity were also used during phasing and refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 2107 5.31 %thin shells (sftools)
Rwork0.2087 ---
obs0.2102 39708 --
Displacement parametersBiso max: 145.4 Å2 / Biso mean: 58.6664 Å2 / Biso min: 16.94 Å2
Baniso -1Baniso -2Baniso -3
1--12.9872 Å20 Å20 Å2
2--1.8498 Å20 Å2
3---11.1374 Å2
Refine analyzeLuzzati coordinate error obs: 0.402 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9156 0 62 0 9218
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d28412
X-RAY DIFFRACTIONt_trig_c_planes1432
X-RAY DIFFRACTIONt_gen_planes14255
X-RAY DIFFRACTIONt_it935720
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion13635
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact101844
X-RAY DIFFRACTIONt_bond_d935720.01
X-RAY DIFFRACTIONt_angle_deg1281921.16
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion18.54
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.2409 2917
all0.2409 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2627-2.11872.74111.4881-1.54430.91780.0261-0.22530.15050.1885-0.0576-0.0406-0.0208-0.00250.03150.22030.0730.0867-0.1583-0.1511-0.008327.620724.734586.4977
23.8972-0.08130.34671.7632-0.96793.1868-0.22920.40170.24770.0402-0.0858-0.4019-0.03690.54420.315-0.1148-0.1099-0.0710.01190.0967-0.147264.5953.148792.9965
32.37060.27190.95121.9175-0.22521.92080.0433-0.0517-0.11550.0369-0.1280.08970.03690.02940.0847-0.0661-0.0077-0.0113-0.04660.0542-0.134940.2601-2.401381.8258
40.7212-2.2411-1.46380.8298-1.890900.0155-0.06910.04460.208-0.0584-0.1211-0.0748-0.17370.04290.1539-0.0228-0.1512-0.0124-0.0693-0.103142.769217.263795.46
56.59251.3198-0.50543.5651-2.4643.15380.06310.3620.54420.50330.41810.5442-0.5345-0.5442-0.4812-0.22580.13960.1502-0.14360.1520.037711.778322.393966.4182
62.78120.309-0.79671.9671-0.98492.83090.0891-0.05730.2410.0903-0.0034-0.037-0.29750.2336-0.0857-0.0458-0.0349-0.0179-0.15230.0104-0.096538.173617.577865.4949
70.08781.9906-0.90691.94461.67961.728-0.02170.11610.07920.0224-0.119-0.09330.05580.01490.14070.29580.06650.1396-0.2482-0.0848-0.043942.9975-29.522838.4485
84.2735-0.04670.04542.183-0.98112.514-0.0548-0.36130.03330.06090.0271-0.5171-0.37780.54420.0277-0.1577-0.12490.03680.1201-0.0988-0.193966.27412.841632.4447
91.9364-0.369-0.85292.01310.58953.6607-0.08240.0669-0.018-0.0077-0.02080.11320.10280.0490.1032-0.043-0.02520.021-0.0988-0.0022-0.147141.143-0.685642.7042
100.1592.9104-0.92630.2824-2.765600.00980.0653-0.09840.03180.07080.04190.22650.0534-0.08060.1679-0.02460.10040.055-0.1059-0.125152.0721-16.243729.8382
114.6492.7648-0.32376.6376-0.95642.3008-0.0525-0.3563-0.0937-0.54420.09250.05640.5442-0.5084-0.040.1785-0.1520.0206-0.29460.0187-0.236324.548-36.127355.6426
122.03231.06220.50532.4742-0.01973.825-0.1316-0.298-0.3281-0.13330.0172-0.24710.490.26910.11430.03950.13380.0776-0.21160.053-0.12546.9912-19.780859.965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|72 - 94}A72 - 94
2X-RAY DIFFRACTION2{A|95 - 231}A95 - 231
3X-RAY DIFFRACTION3{A|232 - 427}A232 - 427
4X-RAY DIFFRACTION4{B|69 - 94}B69 - 94
5X-RAY DIFFRACTION5{B|95 - 231}B95 - 231
6X-RAY DIFFRACTION6{B|232 - 427}B232 - 427
7X-RAY DIFFRACTION7{C|72 - 94}C72 - 94
8X-RAY DIFFRACTION8{C|95 - 231}C95 - 231
9X-RAY DIFFRACTION9{C|232 - 427}C232 - 427
10X-RAY DIFFRACTION10{D|69 - 94}D69 - 94
11X-RAY DIFFRACTION11{D|95 - 229}D95 - 229
12X-RAY DIFFRACTION12{D|232 - 425}D232 - 425

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