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- PDB-4oop: Arabidopsis thaliana dUTPase with with magnesium and alpha,beta-i... -

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Basic information

Entry
Database: PDB / ID: 4oop
TitleArabidopsis thaliana dUTPase with with magnesium and alpha,beta-imido-dUTP
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / dUTPase / hydrolysis / dUTP
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / DNA repair / magnesium ion binding / identical protein binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsInoguchi, N. / Bajaj, M. / Moriyama, H.
CitationJournal: BMC Res Notes / Year: 2015
Title: Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation.
Authors: Inoguchi, N. / Chaiseeda, K. / Yamanishi, M. / Kim, M.K. / Jang, Y. / Bajaj, M. / Chia, C.P. / Becker, D.F. / Moriyama, H.
History
DepositionFeb 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Sep 20, 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 / struct_site
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.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.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.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 / _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: Deoxyuridine 5'-triphosphate nucleotidohydrolase
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2119
Polymers52,7373
Non-polymers1,4746
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13600 Å2
ΔGint-94 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.089, 70.680, 75.064
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 Deoxyuridine 5'-triphosphate nucleotidohydrolase / dUTPase / dUTP pyrophosphatase / dUTP-pyrophosphatase-like 1 / AtDUT1


Mass: 17578.861 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DUT, DUT1, At3g46940, T6H20.30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9STG6, dUTP diphosphatase
#2: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 552 / 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: 1.76 Å3/Da / Density % sol: 30.22 %
Crystal growTemperature: 298 K / pH: 9
Details: 2 M ammonium sulfate, 0.1 M Tris-HCl, 0.02 M Taurine, 5mM dUpNHpp,5mM Magnesium, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9787
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2013
RadiationMonochromator: BENT GE (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.5→31.97 Å / Num. obs: 59499 / % possible obs: 98.5 % / Observed criterion σ(I): 5 / Redundancy: 6.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 46.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 7.7 / % possible all: 97.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1606)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 4OOQ

4ooq


Resolution: 1.5→31.97 Å / SU ML: 0.13 / σ(F): 0 / Phase error: 19.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 1951 3.4 %
Rwork0.174 --
obs0.175 57348 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→31.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 87 552 3658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073169
X-RAY DIFFRACTIONf_angle_d1.1644324
X-RAY DIFFRACTIONf_dihedral_angle_d11.6411143
X-RAY DIFFRACTIONf_chiral_restr0.072495
X-RAY DIFFRACTIONf_plane_restr0.006546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4998-1.53730.24041050.19993631X-RAY DIFFRACTION88
1.5373-1.57890.25341440.18663791X-RAY DIFFRACTION93
1.5789-1.62530.21021230.17973807X-RAY DIFFRACTION93
1.6253-1.67780.21911450.17523808X-RAY DIFFRACTION93
1.6778-1.73770.2241270.17953945X-RAY DIFFRACTION96
1.7377-1.80730.24341340.17673945X-RAY DIFFRACTION95
1.8073-1.88960.19631590.17173947X-RAY DIFFRACTION96
1.8896-1.98920.20271370.16634048X-RAY DIFFRACTION98
1.9892-2.11380.18871430.16924111X-RAY DIFFRACTION99
2.1138-2.27690.19411490.16614117X-RAY DIFFRACTION99
2.2769-2.5060.19831450.17464142X-RAY DIFFRACTION99
2.506-2.86840.2291500.18714153X-RAY DIFFRACTION99
2.8684-3.61310.20831490.16774202X-RAY DIFFRACTION99
3.6131-31.9810.20241410.17293750X-RAY DIFFRACTION85

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