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

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Basic information

Entry
Database: PDB / ID: 5nyz
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.
ComponentsDUTPaseDUTP diphosphatase
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: 2.5 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 CompetitivenessBES-2014-068617 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.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_symmetry

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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)19,6444
Polymers19,1291
Non-polymers5163
Water25214
1
A: DUTPase
hetero molecules

A: DUTPase
hetero molecules

A: DUTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,93312
Polymers57,3863
Non-polymers1,5479
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 area16160 Å2
ΔGint-89 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.270, 87.270, 87.270
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-312-

HOH

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Components

#1: Protein DUTPase / DUTP diphosphatase


Mass: 19128.695 Da / Num. of mol.: 1 / Mutation: D95E
Source method: isolated from a genetically manipulated source
Details: Ordered C-terminal is placed over the nucleotide on active center. Magnesium atom is coordinated by E95 residue.
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.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% Ethanol; 10% Glicerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97921 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.5→87.27 Å / Num. obs: 7924 / % possible obs: 100 % / Redundancy: 18 % / CC1/2: 0.898 / Rpim(I) all: 0.038 / Net I/σ(I): 15.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 18.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 882 / CC1/2: 0.658 / Rpim(I) all: 0.573 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZEZ

3zez


Resolution: 2.5→61.71 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.894 / SU B: 11.95 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.452 / ESU R Free: 0.301 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28055 374 4.7 %RANDOM
Rwork0.22569 ---
obs0.22853 7533 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.162 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.5→61.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1299 0 30 14 1343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191348
X-RAY DIFFRACTIONr_bond_other_d0.0010.021239
X-RAY DIFFRACTIONr_angle_refined_deg1.141.9851826
X-RAY DIFFRACTIONr_angle_other_deg0.82332874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8735165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67924.75461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02615236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.01158
X-RAY DIFFRACTIONr_chiral_restr0.0660.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02257
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_it1.8096.14666
X-RAY DIFFRACTIONr_mcbond_other1.8086.135665
X-RAY DIFFRACTIONr_mcangle_it3.1539.18829
X-RAY DIFFRACTIONr_mcangle_other3.1519.187830
X-RAY DIFFRACTIONr_scbond_it1.6296.435682
X-RAY DIFFRACTIONr_scbond_other1.6316.433681
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8799.568998
X-RAY DIFFRACTIONr_long_range_B_refined5.46168.551316
X-RAY DIFFRACTIONr_long_range_B_other5.3368.5281316
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.501→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 20 -
Rwork0.316 559 -
obs--100 %

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