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- PDB-6dby: Crystal structure of Nudix 1 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 6dby
TitleCrystal structure of Nudix 1 from Arabidopsis thaliana
ComponentsNudix hydrolase 1
KeywordsHYDROLASE / Phosphatase
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 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNoel, J.P. / Thomas, S.T. / Dudareva, N. / Henry, L.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)EEC-0813570 United States
CitationJournal: Nat Plants / Year: 2018
Title: Contribution of isopentenyl phosphate to plant terpenoid metabolism.
Authors: Henry, L.K. / Thomas, S.T. / Widhalm, J.R. / Lynch, J.H. / Davis, T.C. / Kessler, S.A. / Bohlmann, J. / Noel, J.P. / Dudareva, N.
History
DepositionMay 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,3363
Polymers33,3122
Non-polymers241
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-21 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.190, 73.070, 116.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 16655.830 Da / Num. of mol.: 2
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 (E. coli)
References: UniProt: Q9CA40, 8-oxo-dGTP diphosphatase, dihydroneopterin triphosphate diphosphatase, NAD+ diphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M succinic acid pH 5.0 20% PEG 4000 0.3 M magnesium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→61.908 Å / Num. obs: 21377 / % possible obs: 98.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 12.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.206 / Num. unique obs: 1404 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
MOSFLM7.1.0data reduction
Aimless0.3.11data scaling
MOLREPphasing
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KYX

4kyx


Resolution: 2→61.908 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 2091 5.26 %
Rwork0.1858 --
obs0.1878 21321 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→61.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 1 185 2387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072265
X-RAY DIFFRACTIONf_angle_d0.83077
X-RAY DIFFRACTIONf_dihedral_angle_d18.463833
X-RAY DIFFRACTIONf_chiral_restr0.056329
X-RAY DIFFRACTIONf_plane_restr0.005399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04650.338970.2262310X-RAY DIFFRACTION90
2.0465-2.09770.2679960.20242328X-RAY DIFFRACTION89
2.0977-2.15440.19541370.21032554X-RAY DIFFRACTION100
2.1544-2.21780.28771550.21672541X-RAY DIFFRACTION100
2.2178-2.28940.26751470.2242541X-RAY DIFFRACTION100
2.2894-2.37120.25741670.21422495X-RAY DIFFRACTION100
2.3712-2.46620.27551500.21682538X-RAY DIFFRACTION100
2.4662-2.57840.29331340.21282573X-RAY DIFFRACTION100
2.5784-2.71440.22931420.21232539X-RAY DIFFRACTION100
2.7144-2.88440.27551380.21092539X-RAY DIFFRACTION100
2.8844-3.10710.23311300.19442572X-RAY DIFFRACTION100
3.1071-3.41980.2291430.17772533X-RAY DIFFRACTION100
3.4198-3.91460.20131420.15762550X-RAY DIFFRACTION100
3.9146-4.93170.15411440.13642539X-RAY DIFFRACTION100
4.9317-61.93730.16191690.16722518X-RAY DIFFRACTION99

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