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- PDB-5wwd: Crystal structure of AtNUDX1 -

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Basic information

Entry
Database: PDB / ID: 5wwd
TitleCrystal structure of AtNUDX1
ComponentsNudix hydrolase 1
KeywordsHYDROLASE / NUDX1 / Arabidopsis thaliana / 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
METHOXYETHANE / AMMONIUM ION / Nudix hydrolase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.386 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
DepositionDec 31, 2016Deposition 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 ...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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,75814
Polymers33,1662
Non-polymers59212
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-77 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.522, 83.181, 115.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

#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: 16582.779 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9CA40, 8-oxo-dGTP diphosphatase, dihydroneopterin triphosphate diphosphatase, NAD+ diphosphatase

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Non-polymers , 5 types, 395 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-2ME / METHOXYETHANE / Methoxyethane


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
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 PILATUS 6M / Detector: CCD / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.356→41.59 Å / Num. obs: 458092 / % possible obs: 99.9 % / Redundancy: 6.3 % / Net I/σ(I): 25.8

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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: 5GP0

5gp0


Resolution: 1.386→39.12 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1774 3381 4.98 %
Rwork0.1757 --
obs0.1758 67894 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.386→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 35 383 2618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112294
X-RAY DIFFRACTIONf_angle_d1.1193108
X-RAY DIFFRACTIONf_dihedral_angle_d14.537845
X-RAY DIFFRACTIONf_chiral_restr0.086329
X-RAY DIFFRACTIONf_plane_restr0.006401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3857-1.40550.23051340.21592436X-RAY DIFFRACTION93
1.4055-1.42650.20991400.212620X-RAY DIFFRACTION99
1.4265-1.44880.21691300.20482678X-RAY DIFFRACTION99
1.4488-1.47250.18151270.19532624X-RAY DIFFRACTION99
1.4725-1.49790.17861550.1942691X-RAY DIFFRACTION99
1.4979-1.52520.19671520.18562627X-RAY DIFFRACTION100
1.5252-1.55450.17481460.18292654X-RAY DIFFRACTION100
1.5545-1.58620.20831310.18492685X-RAY DIFFRACTION100
1.5862-1.62070.22381340.1762676X-RAY DIFFRACTION100
1.6207-1.65840.1611380.1832684X-RAY DIFFRACTION100
1.6584-1.69990.1931380.18342693X-RAY DIFFRACTION100
1.6999-1.74590.21391400.18342656X-RAY DIFFRACTION100
1.7459-1.79720.15321420.17782695X-RAY DIFFRACTION100
1.7972-1.85520.19481480.18492657X-RAY DIFFRACTION100
1.8552-1.92160.20351270.18222745X-RAY DIFFRACTION99
1.9216-1.99850.16421200.17392692X-RAY DIFFRACTION100
1.9985-2.08940.17041400.172684X-RAY DIFFRACTION100
2.0894-2.19960.15071370.16252717X-RAY DIFFRACTION100
2.1996-2.33740.1861470.1782701X-RAY DIFFRACTION99
2.3374-2.51780.18511480.18492723X-RAY DIFFRACTION100
2.5178-2.77110.19461380.18772739X-RAY DIFFRACTION100
2.7711-3.1720.18551470.1782756X-RAY DIFFRACTION100
3.172-3.99570.15121570.16262765X-RAY DIFFRACTION99
3.9957-39.13570.17081650.16362915X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 0.3619 Å / Origin y: 60.0944 Å / Origin z: 1.4327 Å
111213212223313233
T0.0983 Å20.0007 Å20.0154 Å2-0.1061 Å2-0.0035 Å2--0.1867 Å2
L0.1183 °2-0.0113 °20.2034 °2-0.0485 °2-0.1011 °2--2.3527 °2
S0.0036 Å °-0.001 Å °0.0589 Å °0.0017 Å °-0.008 Å °-0.0049 Å °-0.0739 Å °0.0172 Å °0.0096 Å °
Refinement TLS groupSelection details: all

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