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- PDB-1eu5: STRUCTURE OF E. COLI DUTPASE AT 1.45 A -

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Basic information

Entry
Database: PDB / ID: 1eu5
TitleSTRUCTURE OF E. COLI DUTPASE AT 1.45 A
ComponentsDEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
KeywordsHYDROLASE / distorted 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 nucleotidohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsGonzalez, A. / Larsson, G. / Persson, R. / Cedergren-Zeppezauer, E.
CitationJournal: 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 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _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)16,4873
Polymers16,3031
Non-polymers1842
Water5,783321
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)49,4609
Polymers48,9083
Non-polymers5536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11860 Å2
ΔGint-74 kcal/mol
Surface area15580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.821, 85.821, 60.476
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE / DUTPASE


Mass: 16302.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P06968, dUTP diphosphatase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.5
Details: SUCCINATE PH 5.5, BIS-TRIS, PH 6.2, PEG 8000, EVAPORATION, temperature 277K
Crystal grow
*PLUS
pH: 6.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mMsuccinate11
2100 mMsodium ethylmercurythiosalicylate11
33 mg/mlprotein12
410 mMBis-Tris12
51.5 %PEG800012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.83
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83 Å / Relative weight: 1
ReflectionResolution: 1.45→47 Å / Num. all: 29458 / Num. obs: 29458 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 9.1
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.15 / Num. unique all: 4146 / % possible all: 99.9
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.6

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Processing

Software
NameVersionClassification
ARP/wARPmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.45→41 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The temperature factor of S atoms was refined anisotropically
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 1488 -random
Rwork0.1827 ---
all0.1401 29246 --
obs0.1401 27758 99.3 %-
Refinement stepCycle: LAST / Resolution: 1.45→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 0 12 321 1360
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_bond_d0.012
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 41 Å / σ(I): 3 / σ(F): 0 / % reflection Rfree: 5 % / Num. reflection obs: 24300
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.029
X-RAY DIFFRACTIONs_chiral_restr0.083

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