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- PDB-1syl: Crystal structure of inactive mutant dUTPase complexed with subst... -

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Basic information

Entry
Database: PDB / ID: 1syl
TitleCrystal structure of inactive mutant dUTPase complexed with substrate dUTP
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / enzyme-ligand complex / jelly roll
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'-TRIPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBarabas, O. / Kovari, J. / Pongracz, V. / 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
DepositionApr 1, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)17,0385
Polymers16,3021
Non-polymers7374
Water3,009167
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)51,11515
Polymers48,9053
Non-polymers2,21012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area13240 Å2
ΔGint-87 kcal/mol
Surface area15420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.421, 76.421, 100.259
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-501-

TRS

21A-502-

TRS

31A-1015-

HOH

DetailsThe biological assembly is a hexamer 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: 16301.631 Da / Num. of mol.: 1 / Mutation: D90N
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DUT / DEOXYURIDINE-5'-TRIPHOSPHATE


Mass: 468.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O14P3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.6 Å3/Da / Density % sol: 52.2 %
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: BW7B / Wavelength: 0.8414 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2004 / Details: mirror
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8414 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 13413 / Num. obs: 13413 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 2.88 % / Biso Wilson estimate: 32.959 Å2 / Rsym value: 0.063 / Net I/σ(I): 14.97
Reflection shellResolution: 1.91→2.03 Å / Redundancy: 2.91 % / Mean I/σ(I) obs: 2.54 / Num. unique all: 2085 / Rsym value: 0.484 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EUW

1euw


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.296 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The water molecule HOH107 is only partially occupied as indicated by its weak electron density and relatively high refined B-factor. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The water molecule HOH107 is only partially occupied as indicated by its weak electron density and relatively high refined B-factor. However, the resolution of the structure did not allow sophisticated refinement of water occupancy.
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 645 5 %RANDOM
Rwork0.15821 ---
all0.15971 12350 --
obs0.15971 12350 98.62 %-
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: 29.501 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0.4 Å20 Å2
2---0.8 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 37 167 1239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221101
X-RAY DIFFRACTIONr_bond_other_d0.0020.021029
X-RAY DIFFRACTIONr_angle_refined_deg1.6862.0131497
X-RAY DIFFRACTIONr_angle_other_deg0.83832401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4575136
X-RAY DIFFRACTIONr_chiral_restr0.1040.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021178
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02194
X-RAY DIFFRACTIONr_nbd_refined0.1980.2154
X-RAY DIFFRACTIONr_nbd_other0.2570.21162
X-RAY DIFFRACTIONr_nbtor_other0.0870.2691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.2129
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3660.220
X-RAY DIFFRACTIONr_mcbond_it1.4662686
X-RAY DIFFRACTIONr_mcangle_it3.13741109
X-RAY DIFFRACTIONr_scbond_it10.34420415
X-RAY DIFFRACTIONr_scangle_it13.5550388
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 53
Rwork0.277 884

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