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- PDB-5nz2: Twist and induce: Dissecting the link between the enzymatic activ... -

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Basic information

Entry
Database: PDB / ID: 5nz2
TitleTwist and induce: Dissecting the link between the enzymatic activity and the SaPI inducing capacity of the phage 80 dUTPase. D95E mutant from dUTPase 80alpha phage.
ComponentsDUTPase
KeywordsHYDROLASE / dUTPase / 80 phage / S.aureus
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 / dUTP diphosphatase
Similarity search - Component
Biological speciesStaphylococcus phage 80alpha (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsAlite, C. / Humphrey, S. / Donderis, J. / Maiques, E. / Ciges-Tomas, J.R. / Penades, J.R. / Marina, A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBES2014-068617 Spain
Spanish Ministry of Economy and CompetitivenessBIO2013-42619-P Spain
CitationJournal: Sci Rep / Year: 2017
Title: Dissecting the link between the enzymatic activity and the SaPI inducing capacity of the phage 80 alpha dUTPase.
Authors: Alite, C. / Humphrey, S. / Donderis, J. / Maiques, E. / Ciges-Tomas, J.R. / Penades, J.R. / Marina, A.
History
DepositionMay 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)19,6203
Polymers19,1291
Non-polymers4912
Water37821
1
A: DUTPase
hetero molecules

A: DUTPase
hetero molecules

A: DUTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8609
Polymers57,3863
Non-polymers1,4746
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area12290 Å2
ΔGint-85 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.192, 87.192, 87.192
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-313-

HOH

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Components

#1: Protein DUTPase


Mass: 19128.695 Da / Num. of mol.: 1 / Mutation: D95E
Source method: isolated from a genetically manipulated source
Details: C-terminal not present in the strcutre although nucleotide is placed in the active center. Magnesium atom is not coordinated by E95.
Source: (gene. exp.) Staphylococcus phage 80alpha (virus) / Plasmid: pet28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4ZF98
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 32% Etanol, 2% PEG 1000, 0.1M phosphate citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.85→38.99 Å / Num. obs: 5130 / % possible obs: 96.1 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 5.2
Reflection shellResolution: 2.85→3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.394 / Num. unique obs: 740 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZEZ

3zez


Resolution: 2.85→38.99 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.869 / SU B: 20.197 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.413 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27753 235 4.6 %RANDOM
Rwork0.22832 ---
obs0.2307 4894 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.224 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.85→38.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 29 21 1250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191249
X-RAY DIFFRACTIONr_bond_other_d0.0010.021194
X-RAY DIFFRACTIONr_angle_refined_deg1.041.9861698
X-RAY DIFFRACTIONr_angle_other_deg0.77932745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6425154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4362554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.515215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.198156
X-RAY DIFFRACTIONr_chiral_restr0.0620.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021391
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02269
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_it1.0055.753619
X-RAY DIFFRACTIONr_mcbond_other1.0055.75618
X-RAY DIFFRACTIONr_mcangle_it1.8318.621772
X-RAY DIFFRACTIONr_mcangle_other1.838.625773
X-RAY DIFFRACTIONr_scbond_it0.6495.824630
X-RAY DIFFRACTIONr_scbond_other0.6495.825629
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2268.709927
X-RAY DIFFRACTIONr_long_range_B_refined3.48943.7321251
X-RAY DIFFRACTIONr_long_range_B_other3.37543.751249
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.853→2.927 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 20 -
Rwork0.289 363 -
obs--95.75 %

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