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- PDB-3zf5: Phage dUTPases control transfer of virulence genes by a proto-onc... -

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Basic information

Entry
Database: PDB / ID: 3zf5
TitlePhage dUTPases control transfer of virulence genes by a proto-oncogenic G protein-like mechanism. (Staphylococcus bacteriophage 80alpha dUTPase Y84F mutant with dUpNHpp).
ComponentsDUTPASE
KeywordsHYDROLASE / PATHOGENICITY ISLAND / SAPI INDUCTION / GENE TRANSFER / MOONLIGHTING PROTEINS / G-PROTEIN / P-LOOP
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding
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
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / NICKEL (II) ION / dUTP diphosphatase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS PHAGE 80ALPHA (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTormo-Mas, M.A. / Donderis, J. / Garcia-Caballer, M. / Alt, A. / Mir-Sanchis, I. / Marina, A. / Penades, J.R.
Citation
Journal: Mol.Cell / Year: 2013
Title: Phage Dutpases Control Transfer of Virulence Genes by a Proto-Oncogenic G Protein-Like Mechanism.
Authors: Tormo-Mas, M.A. / Donderis, J. / Garcia-Caballer, M. / Alt, A. / Mir-Sanchis, I. / Marina, A. / Penades, J.R.
#1: Journal: Nature / Year: 2010
Title: Moonlighting Bacteriophage Proteins Derepress Staphylococcal Pathogenicity Islands.
Authors: Tormo-Mas, M.A. / Mir, I. / Shrestha, A. / Tallent, S.M. / Campoy, S. / Lasa, I. / Barbe, J. / Novick, R.P. / Christie, G.E. / Penades, J.R.
History
DepositionDec 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Apr 3, 2013Group: Other / Refinement description / Structure summary
Revision 1.3Apr 17, 2013Group: Database references / Other / Structure summary
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: DUTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2605
Polymers22,6521
Non-polymers6094
Water55831
1
A: DUTPASE
hetero molecules

A: DUTPASE
hetero molecules

A: DUTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,78115
Polymers67,9553
Non-polymers1,82712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
Buried area17610 Å2
ΔGint-121.2 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.240, 88.240, 88.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1172-

NI

21A-2015-

HOH

31A-2019-

HOH

41A-2020-

HOH

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Components

#1: Protein DUTPASE


Mass: 22651.627 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: STRUCTURE IN PRESENCE OF DUMP / Source: (gene. exp.) STAPHYLOCOCCUS PHAGE 80ALPHA (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4ZF98, dUTP diphosphatase
#2: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.75 % / Description: NONE
Crystal growDetails: 2-8% TERT-BUTANOL, 0.1M TRIS (PH 8.5), 30-50% MPD PR PEG400.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→14.9 Å / Num. obs: 4719 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 0.35
Reflection shellResolution: 3→3.16 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZEZ

3zez


Resolution: 3.2→14.71 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.807 / SU B: 15.769 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INITIAL MET IS NOT TRACED. RESIDUES F115, K117, E118 AND E159 ARE TRACED AS A BECAUSE OF LACK OF ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.27663 150 4.2 %RANDOM
Rwork0.22189 ---
obs0.22421 3391 89.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.684 Å2
Baniso -1Baniso -2Baniso -3
1-13.46 Å2-0.24 Å2-26.9 Å2
2---8.92 Å2-0.18 Å2
3----4.54 Å2
Refinement stepCycle: LAST / Resolution: 3.2→14.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 31 31 1366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0191353
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8581.9861831
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1155168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.85924.65558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21115242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.058158
X-RAY DIFFRACTIONr_chiral_restr0.0520.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021988
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3293.006675
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6244.509842
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.1113.021678
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.201→3.284 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 16 -
Rwork0.306 265 -
obs--98.25 %

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