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- PDB-1rn8: Crystal structure of dUTPase complexed with substrate analogue im... -

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Basic information

Entry
Database: PDB / ID: 1rn8
TitleCrystal structure of dUTPase complexed with substrate analogue imido-dUTP
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / Jelly Roll / Enzyme-ligand complex
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / protein homotrimerization / magnesium ion binding / protein-containing complex / identical protein binding / cytosol
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
ACETATE ION / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsBarabas, O. / Pongracz, V. / Kovari, J. / Wilmanns, M. / Vertessy, B.G.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Structural Insights into the Catalytic Mechanism of Phosphate Ester Hydrolysis by dUTPase.
Authors: Barabas, O. / Pongracz, V. / Kovari, J. / Wilmanns, M. / Vertessy, B.G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Atomic resolution structure of Escherichia coli dUTPase determined ab initio
Authors: Gonzalez, A. / Larsson, G. / Persson, R. / Cedergren-Zeppezauer, E.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN THE TRIS MOLECULES (TRS), WHICH HAVE INHERENT THREEFOLD SYMMETRY, ARE LOCATED ON A ...HETEROGEN THE TRIS MOLECULES (TRS), WHICH HAVE INHERENT THREEFOLD SYMMETRY, ARE LOCATED ON A CRYSTALLOGRAPHIC THREEFOLD AXIS IN THE PRESENT STRUCTURE. IN AN ASYMMETRIC UNIT THERE IS ONLY ONE THIRD OF THE MOLECULES AND THE COMPLETE MOLECULES ARE BUILT BY THREEFOLD CRYSTALLOGRAPHIC SYMMETRY IN THE CRYSTAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9755
Polymers16,3031
Non-polymers6734
Water3,441191
1
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,92615
Polymers48,9083
Non-polymers2,01812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)74.618, 74.618, 99.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-800-

TRS

21A-1023-

HOH

31A-1156-

HOH

41A-1157-

HOH

51A-1158-

HOH

61A-1159-

HOH

71A-1176-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: 1-y, 1+x-y, z and -x+y, 1-x, z.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Deoxyuridine 5'-triphosphate nucleotidohydrolase / dUTPase / dUTP pyrophosphatase


Mass: 16302.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DUT, DNAS, SOF, B3640 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06968, dUTP diphosphatase

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Non-polymers , 5 types, 195 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.54 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG 3350, sodium acetate, Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 25, 2002
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.93→27.1 Å / Num. obs: 12768 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rsym value: 0.061 / Net I/σ(I): 10.3
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 7.56 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 819 / Rsym value: 0.268 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EUW

1euw


Resolution: 1.93→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.467 / SU ML: 0.072 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18017 624 4.9 %RANDOM
Rwork0.13701 ---
all0.164 12144 --
obs0.13906 12144 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.402 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å20 Å2
2--0.11 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.93→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 37 191 1317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221143
X-RAY DIFFRACTIONr_bond_other_d0.0080.021078
X-RAY DIFFRACTIONr_angle_refined_deg1.6032.0141553
X-RAY DIFFRACTIONr_angle_other_deg0.86932511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0065137
X-RAY DIFFRACTIONr_chiral_restr0.090.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021212
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02205
X-RAY DIFFRACTIONr_nbd_refined0.1910.2169
X-RAY DIFFRACTIONr_nbd_other0.2590.21150
X-RAY DIFFRACTIONr_nbtor_other0.0850.2637
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3550.2152
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.252
X-RAY DIFFRACTIONr_mcbond_it2.7334704
X-RAY DIFFRACTIONr_mcangle_it4.827101138
X-RAY DIFFRACTIONr_scbond_it7.27410439
X-RAY DIFFRACTIONr_scangle_it9.88920415
LS refinement shellResolution: 1.931→1.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 46 -
Rwork0.17 763 -
obs-819 99.2 %

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