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- PDB-5wy6: Crystal structure of AtNUDX1 (E56A) -

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Basic information

Entry
Database: PDB / ID: 5wy6
TitleCrystal structure of AtNUDX1 (E56A)
ComponentsNudix hydrolase 1
KeywordsHYDROLASE / NUDX1 / E56A mutant / apo
Function / homology
Function and homology information


dihydroneopterin triphosphate diphosphatase / dihydroneopterin triphosphate pyrophosphohydrolase activity / NAD+ diphosphatase / NAD+ diphosphatase activity / NADH pyrophosphatase activity / 8-oxo-dGTP diphosphatase / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA damage response / metal ion binding / cytosol
Similarity search - Function
NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Nudix hydrolase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.779 Å
AuthorsLiu, J. / Guan, Z. / Yan, L. / Zou, T. / Yin, P.
CitationJournal: Mol Plant / Year: 2018
Title: Structural Insights into the Substrate Recognition Mechanism of Arabidopsis GPP-Bound NUDX1 for Noncanonical Monoterpene Biosynthesis.
Authors: Liu, J. / Guan, Z. / Liu, H. / Qi, L. / Zhang, D. / Zou, T. / Yin, P.
History
DepositionJan 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Nudix hydrolase 1
A: Nudix hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6488
Polymers33,0492
Non-polymers5996
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-11 kcal/mol
Surface area15110 Å2
Unit cell
Length a, b, c (Å)84.658, 117.306, 68.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Nudix hydrolase 1 / / AtNUDT1 / 7 / 8-dihydro-8-oxoguanine-triphosphatase / 8-oxo-dGTP diphosphatase / 8-oxo-dGTPase / ...AtNUDT1 / 7 / 8-dihydro-8-oxoguanine-triphosphatase / 8-oxo-dGTP diphosphatase / 8-oxo-dGTPase / Dihydroneopterin triphosphate diphosphatase / Dihydroneopterin triphosphate pyrophosphohydrolase / DHNTP pyrophosphohydrolase / NADH pyrophosphatase


Mass: 16524.742 Da / Num. of mol.: 2 / Mutation: E56A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NUDT1, NUDX1, At1g68760, F14K14.13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9CA40, 8-oxo-dGTP diphosphatase, dihydroneopterin triphosphate diphosphatase, NAD+ diphosphatase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / 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.: 167 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: Sodium acetate trihydrate, PEG 2000, Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: CCD / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.668→45 Å / Num. obs: 244523 / % possible obs: 99.4 % / Redundancy: 6.1 % / Net I/σ(I): 18.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data collection
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WWD

5wwd


Resolution: 1.779→44.672 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 1648 4.96 %
Rwork0.196 --
obs0.1968 33210 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.779→44.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 38 167 2397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062302
X-RAY DIFFRACTIONf_angle_d0.7693118
X-RAY DIFFRACTIONf_dihedral_angle_d15.193849
X-RAY DIFFRACTIONf_chiral_restr0.057330
X-RAY DIFFRACTIONf_plane_restr0.005401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7786-1.83090.28381450.24952540X-RAY DIFFRACTION98
1.8309-1.890.2681470.22962603X-RAY DIFFRACTION100
1.89-1.95760.24761420.21332602X-RAY DIFFRACTION100
1.9576-2.0360.2431530.2072573X-RAY DIFFRACTION100
2.036-2.12860.25051330.19922641X-RAY DIFFRACTION100
2.1286-2.24080.24641150.19732596X-RAY DIFFRACTION100
2.2408-2.38120.22371320.20592640X-RAY DIFFRACTION100
2.3812-2.56510.26931350.20182618X-RAY DIFFRACTION100
2.5651-2.82320.28241500.19962628X-RAY DIFFRACTION100
2.8232-3.23160.18421330.18122668X-RAY DIFFRACTION100
3.2316-4.0710.17661370.17712667X-RAY DIFFRACTION100
4.071-44.6860.17981260.19982786X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.1939 Å / Origin y: 14.4057 Å / Origin z: 48.9083 Å
111213212223313233
T0.1969 Å20.0318 Å20.0047 Å2-0.1944 Å20.0023 Å2--0.239 Å2
L0.3308 °2-0.0215 °2-0.0302 °2-0.8507 °20.1627 °2--1.3653 °2
S0.0028 Å °0.0409 Å °-0.007 Å °-0.0677 Å °-0.0053 Å °0.0802 Å °0.013 Å °-0.1058 Å °0.0022 Å °
Refinement TLS groupSelection details: all

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