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- PDB-3ecy: Crystal structural analysis of Drosophila melanogaster dUTPase -

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Basic information

Entry
Database: PDB / ID: 3ecy
TitleCrystal structural analysis of Drosophila melanogaster dUTPase
ComponentsCG4584-PA, isoform A (BcDNA.LD08534)
KeywordsHYDROLASE / jelly-roll / dimeric assembly
Function / homology
Function and homology information


Interconversion of nucleotide di- and triphosphates / dUTP metabolic process / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm
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 speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsTakacs, E. / Barabas, O. / Vertessy, B.G.
CitationJournal: Febs Lett. / Year: 2009
Title: Molecular shape and prominent role of beta-strand swapping in organization of dUTPase oligomers.
Authors: Takacs, E. / Barabas, O. / Petoukhov, M.V. / Svergun, D.I. / Vertessy, B.G.
History
DepositionSep 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CG4584-PA, isoform A (BcDNA.LD08534)
B: CG4584-PA, isoform A (BcDNA.LD08534)


Theoretical massNumber of molelcules
Total (without water)34,7082
Polymers34,7082
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-25 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.799, 42.799, 169.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein CG4584-PA, isoform A (BcDNA.LD08534)


Mass: 17353.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dUTPase, BcDNA.LD08534, CG4584, Dmel_CG4584 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9V3I1, dUTP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 50 mM sodium succinate buffer, 200 mM sodium chloride, 30-35% methyl-pentane diol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8457 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: Si [111], horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8457 Å / Relative weight: 1
ReflectionResolution: 1.78→20 Å / Num. all: 28229 / Num. obs: 28229 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7.45 % / Biso Wilson estimate: 41.2 Å2 / Rsym value: 0.068 / Net I/σ(I): 14.95
Reflection shellResolution: 1.78→1.89 Å / Redundancy: 6.84 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4348 / Rsym value: 0.74 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q5U

1q5u


Resolution: 1.88→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.337 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22221 1225 5 %RANDOM
Rwork0.20048 ---
obs0.20152 23345 99.77 %-
all-23345 --
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: 41.067 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--0.62 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 0 111 1881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221831
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.9612492
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.845244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79224.21176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14315288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0381510
X-RAY DIFFRACTIONr_chiral_restr0.1380.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021386
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.2659
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21264
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2124
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.172.51213
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0963.51914
X-RAY DIFFRACTIONr_scbond_it4.4714678
X-RAY DIFFRACTIONr_scangle_it7.06925573
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 96 -
Rwork0.272 1688 -
obs-29721 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.06480.1954-0.2971.3114-0.75141.3905-0.00770.0491-0.00760.1326-0.04280.0012-0.14970.14420.0506-0.11360.0382-0.0568-0.0526-0.0029-0.054916.99616.999310.8163
20.1014-0.1146-0.30631.24410.68311.0569-0.0051-0.0606-0.026-0.1445-0.0318-0.0471-0.125-0.08970.0369-0.1238-0.0285-0.0553-0.07560.0057-0.08125.78746.9752-10.8117
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 14419 - 144
2X-RAY DIFFRACTION2BB19 - 14419 - 144

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