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- PDB-3zf4: Phage dUTPases control transfer of virulence genes by a proto- on... -

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Basic information

Entry
Database: PDB / ID: 3zf4
TitlePhage dUTPases control transfer of virulence genes by a proto- oncogenic G protein-like mechanism. (Staphylococcus bacteriophage 80alpha dUTPase Y81A mutant with dUpNHpp).
ComponentsDUTPASEDUTP diphosphatase
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: DUTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1845
Polymers22,5761
Non-polymers6094
Water21612
1
A: DUTPASE
hetero molecules

A: DUTPASE
hetero molecules

A: DUTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,55315
Polymers67,7273
Non-polymers1,82712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area16100 Å2
ΔGint-116 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.470, 87.470, 87.470
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-1170-

NI

21A-1171-

NI

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Components

#1: Protein DUTPASE / DUTP diphosphatase


Mass: 22575.529 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: STRUCTURE IN PRESENCE OF DUPNHPP AND MAGNESIUM / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.44 Å3/Da / Density % sol: 49.6 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→61.9 Å / Num. obs: 4224 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.2
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

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

3zez


Resolution: 3.1→61.85 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.89 / SU B: 24.204 / SU ML: 0.424 / Cross valid method: THROUGHOUT / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INITIAL MET IS NOT TRACED. RESIDUES K143 AND V170 ARE NOT TRACED BECAUSE OF LACK OF ELECTRON DENSITY. RESIUDES E159, , R160, K163, G169 ARE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INITIAL MET IS NOT TRACED. RESIDUES K143 AND V170 ARE NOT TRACED BECAUSE OF LACK OF ELECTRON DENSITY. RESIUDES E159, , R160, K163, G169 ARE TRACED AS A. RESIDUES S156-S158 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.29059 521 12.4 %RANDOM
Rwork0.24025 ---
obs0.24698 3692 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 105.915 Å2
Baniso -1Baniso -2Baniso -3
1--39.57 Å216.24 Å2-72.18 Å2
2---42.35 Å2-56 Å2
3---81.93 Å2
Refinement stepCycle: LAST / Resolution: 3.1→61.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1275 0 31 12 1318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0191321
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9221.9881784
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0715161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5172558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18615239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.605157
X-RAY DIFFRACTIONr_chiral_restr0.0550.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021959
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_it1.69410.596653
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.04815.875811
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.38110.771668
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: 3.102→3.182 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 43 -
Rwork0.352 261 -
obs--100 %

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