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- PDB-2hr6: Crystal structure of dUTPase in complex with substrate analogue d... -

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Basic information

Entry
Database: PDB / ID: 2hr6
TitleCrystal structure of dUTPase in complex with substrate analogue dUDP and manganese
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / JELLY ROLL / ENZYME-LIGAND-metal 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
DEOXYURIDINE-5'-DIPHOSPHATE / : / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsBarabas, O. / Kovari, J. / Tapai, R. / Vertessy, B.G.
Citation
Journal: Proteins / Year: 2008
Title: Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site.
Authors: Kovari, J. / Barabas, O. / Varga, B. / Bekesi, A. / Tolgyesi, F. / Fidy, J. / Nagy, J. / Vertessy, B.G.
#1: 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.
#2: 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
DepositionJul 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Aug 30, 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 / diffrn_source / pdbx_initial_refinement_model / 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_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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,8084
Polymers16,3031
Non-polymers5053
Water2,810156
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)50,42312
Polymers48,9083
Non-polymers1,5169
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
Buried area12690 Å2
ΔGint-89 kcal/mol
Surface area15910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.049, 75.049, 99.936
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-1089-

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

#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 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06968, dUTP diphosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-DUD / DEOXYURIDINE-5'-DIPHOSPHATE


Mass: 388.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O11P2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 20% PEG 3350, 0.2M SODIUM ACETATE, 0.1M 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: MAR CCD 165 mm / Detector: CCD / Date: Mar 17, 2002 / Details: mirror
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.84→24.9 Å / Num. all: 14703 / Num. obs: 14703 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Biso Wilson estimate: 22.35 Å2 / Rsym value: 0.064 / Net I/σ(I): 10.8
Reflection shellResolution: 1.84→1.89 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 815 / Rsym value: 0.558 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUW

1euw


Resolution: 1.84→24.9 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.48 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17338 749 5.1 %RANDOM
Rwork0.15054 ---
all0.15168 13953 --
obs0.15168 13953 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.763 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å20 Å2
2---0.09 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.84→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1013 0 29 156 1198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221073
X-RAY DIFFRACTIONr_bond_other_d0.0020.021005
X-RAY DIFFRACTIONr_angle_refined_deg1.7022.011465
X-RAY DIFFRACTIONr_angle_other_deg0.82132326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3224.61539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12115168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.193155
X-RAY DIFFRACTIONr_chiral_restr0.0980.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021180
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02196
X-RAY DIFFRACTIONr_nbd_refined0.2150.2122
X-RAY DIFFRACTIONr_nbd_other0.1910.2888
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2490
X-RAY DIFFRACTIONr_nbtor_other0.0820.2626
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2840.217
X-RAY DIFFRACTIONr_mcbond_it2.232714
X-RAY DIFFRACTIONr_mcbond_other0.0932282
X-RAY DIFFRACTIONr_mcangle_it3.606101107
X-RAY DIFFRACTIONr_scbond_it6.0120410
X-RAY DIFFRACTIONr_scangle_it7.99350356
LS refinement shellResolution: 1.842→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 58 -
Rwork0.189 832 -
obs-890 82.64 %
Refinement TLS params.Method: refined / Origin x: 0.1866 Å / Origin y: 31.3803 Å / Origin z: 4.8255 Å
111213212223313233
T-0.0609 Å2-0.0048 Å20.0184 Å2--0.0529 Å2-0.0189 Å2---0.0563 Å2
L0.2476 °2-0.0981 °2-0.0217 °2-0.808 °2-0.0553 °2--0.1993 °2
S-0.0404 Å °0.0061 Å °-0.0466 Å °-0.0298 Å °-0.0114 Å °-0.0463 Å °0.0264 Å °0.01 Å °0.0518 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1371 - 137
2X-RAY DIFFRACTION1AC7771

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