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- PDB-3fxt: Crystal structure of the N-terminal domain of human NUDT6 -

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Basic information

Entry
Database: PDB / ID: 3fxt
TitleCrystal structure of the N-terminal domain of human NUDT6
ComponentsNucleoside diphosphate-linked moiety X motif 6
KeywordsGENE REGULATION / NUDIX / NUDT6 / GFG / FGF2AS / Antisense basic fibroblast growth factor / FGF-2 regulation / Hydrolase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


NADH pyrophosphatase activity / ADP-ribose diphosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / negative regulation of cell cycle / NAD binding / negative regulation of cell population proliferation / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Nudix hydrolase 6-like / Pre-nudix hydrolase domain / Nudix hydrolase domain / NUDIX hydrolase, conserved site / Nudix box signature. / Gcn5-related N-acetyltransferase (GNAT) / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Nudix hydrolase 6-like / Pre-nudix hydrolase domain / Nudix hydrolase domain / NUDIX hydrolase, conserved site / Nudix box signature. / Gcn5-related N-acetyltransferase (GNAT) / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside diphosphate-linked moiety X motif 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsTresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Schueler, H. / Siponen, M.I. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Wikstrom, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the N-terminal domain of human NUDT6
Authors: Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / ...Authors: Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Schueler, H. / Siponen, M.I. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Wikstrom, M. / Wisniewska, M. / Nordlund, P.
History
DepositionJan 21, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate-linked moiety X motif 6
B: Nucleoside diphosphate-linked moiety X motif 6
C: Nucleoside diphosphate-linked moiety X motif 6
D: Nucleoside diphosphate-linked moiety X motif 6
E: Nucleoside diphosphate-linked moiety X motif 6
F: Nucleoside diphosphate-linked moiety X motif 6
G: Nucleoside diphosphate-linked moiety X motif 6
H: Nucleoside diphosphate-linked moiety X motif 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,73014
Polymers101,1778
Non-polymers5536
Water6,377354
1
A: Nucleoside diphosphate-linked moiety X motif 6
E: Nucleoside diphosphate-linked moiety X motif 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3863
Polymers25,2942
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoside diphosphate-linked moiety X motif 6
G: Nucleoside diphosphate-linked moiety X motif 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3863
Polymers25,2942
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Nucleoside diphosphate-linked moiety X motif 6
hetero molecules

C: Nucleoside diphosphate-linked moiety X motif 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4794
Polymers25,2942
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z+1/31
4
D: Nucleoside diphosphate-linked moiety X motif 6
H: Nucleoside diphosphate-linked moiety X motif 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4794
Polymers25,2942
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: Nucleoside diphosphate-linked moiety X motif 6
hetero molecules

F: Nucleoside diphosphate-linked moiety X motif 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4794
Polymers25,2942
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_664-x+y+1,-x+1,z-1/31
Buried area1680 Å2
ΔGint-14 kcal/mol
Surface area10090 Å2
Unit cell
Length a, b, c (Å)185.800, 185.800, 129.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11E-152-

HOH

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Components

#1: Protein
Nucleoside diphosphate-linked moiety X motif 6 / Nudix motif 6 / Protein GFG / GFG-1 / Antisense basic fibroblast growth factor


Mass: 12647.166 Da / Num. of mol.: 8 / Fragment: N-terminal domain, UNP residues 45-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF2AS, NUDT6 / Plasmid: pNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: P53370
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.1861.34
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, hanging drop7.519% PEG2000 MME, 0.1M Tris-HCl, 0.25M Trimethylamine. Chymotrypsin was added prior to crystallization to a ratio protease:protein of 1:100., pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2772vapor diffusion, hanging drop7.519% PEG2000 MME, 0.1M Tris-HCl, 0.3M Trimethylamine. Chymotrypsin was added prior to crystallization to a ratio protease:protein of 1:100. Crystal was then soaked for 17h in 10% PEG 2000MME, 0.1M Tris-HCl, 0.3M Trimethylamine and 1mM HgAc., pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2773vapor diffusion, hanging drop7.514% PEG2000 MME, 0.1M Tris-HCl. Chymotrypsin was added prior to crystallization to a ratio protease:protein of 1:100. Crystal was then soaked for 2weeks 10% PEG 2000MME, 0.1M Tris-HCl, 0.3M Trimethylamine and 1mM SmCl3., pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Nov 21, 2008 / Details: MIRRORS
RadiationMonochromator: Si(111)monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. all: 58581 / Num. obs: 58279 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.05 % / Rmerge(I) obs: 0.091 / Rsym value: 0.115 / Net I/σ(I): 17.09
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 6.66 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 3.08 / Num. unique all: 4241 / Rsym value: 0.658 / % possible all: 99.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
autoSHARPphasing
REFMAC5.5.0035refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→33.88 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.808 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS REFINMENT / Cross valid method: THROUGHOUT / σ(I): -3 / ESU R: 0.208 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23539 2957 5.1 %RANDOM
Rwork0.20112 ---
all0.20286 55426 --
obs0.20286 55426 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.082 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5594 0 36 354 5984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215870
X-RAY DIFFRACTIONr_bond_other_d0.0010.024053
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.9337958
X-RAY DIFFRACTIONr_angle_other_deg2.19939738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2755742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0222.257288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9215962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7841566
X-RAY DIFFRACTIONr_chiral_restr0.0620.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026634
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021348
X-RAY DIFFRACTIONr_mcbond_it0.521.53586
X-RAY DIFFRACTIONr_mcbond_other0.0331.51470
X-RAY DIFFRACTIONr_mcangle_it0.99825690
X-RAY DIFFRACTIONr_scbond_it1.15732284
X-RAY DIFFRACTIONr_scangle_it2.0394.52252
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 177 -
Rwork0.285 4037 -
obs-4037 100 %
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)
16.8499-1.17571.05930.81420.36171.17230.24060.34660.1594-0.0205-0.1519-0.0266-0.0849-0.0151-0.08870.39830.11830.09660.36720.08740.364690.85437.53227.899
21.7709-0.69560.6491.04860.1121.73390.05040.13530.15110.0245-0.1038-0.07810.0440.12160.05350.4340.16850.12090.38070.12430.357990.90938.74118.833
33.98913.44453.17735.89343.48752.8291-0.04310.07250.2373-0.4176-0.17970.6077-0.330.01230.22290.50980.0675-0.08820.2612-0.0230.456372.92918.62939.558
41.31361.24720.02533.36340.13691.48830.0444-0.0378-0.1653-0.0643-0.0693-0.0283-0.17920.07490.0250.41030.0345-0.03720.2423-0.05130.419877.22110.643.055
55.3656-1.609-1.6321.21020.37684.0924-0.2016-0.2499-0.10040.18060.15340.03960.4928-0.12880.04820.35620.07010.02180.35990.01220.316762.92551.32424.514
63.47570.038-1.08931.1106-0.27454.5276-0.0969-0.20510.07520.06250.1190.09840.1718-0.2589-0.02220.26230.06990.01130.3876-0.03640.349363.69457.70715.868
71.5915-2.49642.00215.9206-3.92653.9012-0.0411-0.06430.0291-0.0064-0.0195-0.3293-0.2353-0.15050.06060.4120.0550.08090.22990.08980.421109.05218.33427.072
87.8115-1.72972.94637.0078-2.6753.815-0.03340.1215-0.0611-0.9497-0.1154-0.33890.19250.05990.14880.60450.06710.16240.1630.06850.3427110.56112.8418.845
94.1338-5.3041.705913.99472.8074.56070.03750.036-0.3075-0.29450.01620.43270.077-0.3142-0.05370.5393-0.10880.13960.3964-0.00620.376476.98926.856-7.958
102.10210.16930.10311.14650.62962.11-0.1578-0.1098-0.2304-0.0838-0.00330.08110.2341-0.11460.1610.46370.10230.11790.31180.05130.386678.67131.1471.49
119.56437.0062.989710.81450.31635.24610.08520.50820.2683-0.0119-0.0507-0.1415-0.1311-0.1278-0.03450.40330.0720.09110.30940.09030.303691.9438.24335.899
122.76170.42221.42021.0698-0.17022.5318-0.13-0.03410.0537-0.0350.08930.1471-0.2031-0.13460.04070.4110.01250.02440.23750.02880.369393.67335.44344.687
135.2253-2.6747-5.93864.36916.026523.0726-0.0322-0.4977-0.50910.33630.2753-0.08640.82360.4556-0.24320.4738-0.04950.19840.13930.06270.605460.697-13.08557.053
142.9023-0.3194-0.42562.89331.00753.054-0.0928-0.1175-0.23670.2857-0.05050.53550.3353-0.19680.14340.3820.00080.07080.1786-0.04340.571162.932-5.51950.255
156.39793.14681.02138.6175-1.02580.50730.23851.2188-0.4752-1.45330.11510.57230.44480.3599-0.35361.13990.37250.46490.7362-0.18160.876129.279-7.64810.539
161.966-1.06420.40053.5177-1.33943.98380.14660.29720.2589-1.2496-0.5776-1.09610.68840.60760.4310.72260.28250.5480.25250.25510.6399125.598-0.37318.185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 64
2X-RAY DIFFRACTION2A65 - 131
3X-RAY DIFFRACTION3B43 - 68
4X-RAY DIFFRACTION4B69 - 131
5X-RAY DIFFRACTION5C42 - 92
6X-RAY DIFFRACTION6C93 - 131
7X-RAY DIFFRACTION7D43 - 103
8X-RAY DIFFRACTION8D104 - 130
9X-RAY DIFFRACTION9E42 - 56
10X-RAY DIFFRACTION10E57 - 130
11X-RAY DIFFRACTION11F42 - 52
12X-RAY DIFFRACTION12F53 - 131
13X-RAY DIFFRACTION13G43 - 54
14X-RAY DIFFRACTION14G55 - 130
15X-RAY DIFFRACTION15H44 - 55
16X-RAY DIFFRACTION16H56 - 130

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