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- PDB-5myi: Convergent evolution involving dimeric and trimeric dUTPases in s... -

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Basic information

Entry
Database: PDB / ID: 5myi
TitleConvergent evolution involving dimeric and trimeric dUTPases in signalling.
ComponentsdUTPase from DI S. aureus phage
KeywordsHYDROLASE / Staphylococcus aureus / pathogenicity island / SaPI / dUTPases / signalling / gene transfer / mobile genetic elements
Function / homologyDimeric dUTPase Dut-like / dUTPase/dCTP pyrophosphatase / dUTPase / dUTP diphosphatase / dUTP diphosphatase activity / DI(HYDROXYETHYL)ETHER / dUTPase from DI S. aureus phage
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDonderis, J. / Bowring, J. / Maiques, E. / Ciges-Tomas, J.R. / Alite, C. / Mehmedov, I. / Tormo-Mas, M.A. / Penades, J.R. / Marina, A.
CitationJournal: PLoS Pathog. / Year: 2017
Title: Convergent evolution involving dimeric and trimeric dUTPases in pathogenicity island mobilization.
Authors: Donderis, J. / Bowring, J. / Maiques, E. / Ciges-Tomas, J.R. / Alite, C. / Mehmedov, I. / Tormo-Mas, M.A. / Penades, J.R. / Marina, A.
History
DepositionJan 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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.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
D: dUTPase from DI S. aureus phage
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6568
Polymers24,1981
Non-polymers4587
Water1,856103
1
D: dUTPase from DI S. aureus phage
hetero molecules

D: dUTPase from DI S. aureus phage
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,31316
Polymers48,3962
Non-polymers91714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area2790 Å2
ΔGint-78 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.450, 79.450, 125.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules D

#1: Protein dUTPase from DI S. aureus phage


Mass: 24198.186 Da / Num. of mol.: 1 / Mutation: A73L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A2D0TC88*PLUS, dUTP diphosphatase

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Non-polymers , 5 types, 110 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% PEG400 0.2 M MgCl2, 0.1 M Hepes 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97948 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.9→68.81 Å / Num. obs: 19182 / % possible obs: 99.9 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2723 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→60.367 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.66
RfactorNum. reflection% reflection
Rfree0.2087 984 5.14 %
Rwork0.1651 --
obs0.1672 19129 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→60.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1365 0 25 103 1493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071432
X-RAY DIFFRACTIONf_angle_d0.9241934
X-RAY DIFFRACTIONf_dihedral_angle_d13.799532
X-RAY DIFFRACTIONf_chiral_restr0.038208
X-RAY DIFFRACTIONf_plane_restr0.005252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-2.00030.27171320.22522534X-RAY DIFFRACTION100
2.0003-2.12570.25551470.20222518X-RAY DIFFRACTION100
2.1257-2.28980.22841410.16212546X-RAY DIFFRACTION100
2.2898-2.52020.21621530.16372540X-RAY DIFFRACTION100
2.5202-2.88490.19421390.172567X-RAY DIFFRACTION100
2.8849-3.63460.22491290.16242650X-RAY DIFFRACTION100
3.6346-60.39790.18251430.15272790X-RAY DIFFRACTION100
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)
10.0159-0.0125-0.01770.0194-0.00980.01250.44980.11050.3649-0.454-0.0112-0.2775-0.3914-0.0515-0.00210.45760.0256-0.11350.2907-0.05450.477133.128650.23132.0215
20.71550.07330.06780.2363-0.03230.3712-0.03390.93720.6082-0.0621-0.2732-0.1922-0.32120.1144-0.02120.3315-0.0318-0.04840.36230.07180.294941.167940.6919-10.0213
30.3846-0.063-0.42330.027-0.05161.0094-0.22630.5653-0.1160.1935-0.09220.13350.98360.0788-0.01450.28190.1304-0.03060.5767-0.03280.232647.609625.9912-11.3538
40.1288-0.18220.05450.2125-0.06930.08320.02770.1674-0.04430.0604-0.1028-0.16130.04580.29660.00020.1862-0.0184-0.03660.21080.00890.194243.233329.46056.0258
50.12230.0537-0.00490.05810.0431-0.01050.0969-0.0204-0.24430.016-0.1050.15920.09750.0912-0.00020.2947-0.039-0.01250.2689-0.01980.272447.353435.609722.4726
60.3796-0.0007-0.1919-0.0379-0.0290.1036-0.05260.13960.1217-0.0928-0.03390.077-0.22690.1993-0.00010.24620.0028-0.03060.23040.00690.263542.95336.29010.9662
70.1236-0.0682-0.0610.0802-0.01120.0319-0.0150.1716-0.0722-0.1513-0.47650.49-0.4309-0.3393-0.00560.29190.0653-0.08740.3526-0.06770.344226.566438.4069-5.5711
80.02840.0088-0.03770.00780.00440.04410.3237-0.21960.32990.0089-0.18210.5229-0.2861-0.6898-0.00010.36250.1086-0.0120.5861-0.05190.368424.885938.265210.6046
90.00030.0094-0.00160.00840.0060.0262-0.30870.00190.31630.27630.1114-0.2364-0.36670.06410.00050.34530.0705-0.07290.3258-0.05830.30833.476837.589618.0089
100.1150.1287-0.03090.1469-0.07830.1145-0.0851-0.0755-0.0995-0.06280.00230.0488-0.2671-0.23020.00020.2375-0.0197-0.0040.326-0.00990.265734.549327.050313.5474
110.0256-0.01580.02680.0116-0.025-0.00940.0554-0.2705-0.6112-0.0099-0.51320.54081.251-0.2536-0.00060.5273-0.01170.05270.33270.03950.420431.016722.28742.1602
120.0355-0.12010.00920.0987-0.0407-0.0111-0.013-0.12050.1559-0.153-0.05140.0388-0.1793-0.1878-0.00030.22940.038-0.05040.2714-0.05510.249734.085638.72845.444
130.40070.15150.5110.24410.04850.45350.02980.48360.2854-0.2243-0.0887-0.2493-0.25890.1476-0.00010.3214-0.0408-0.02390.33180.02940.376649.150943.149-3.3297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 6 )
2X-RAY DIFFRACTION2chain 'D' and (resid 7 through 23 )
3X-RAY DIFFRACTION3chain 'D' and (resid 24 through 28 )
4X-RAY DIFFRACTION4chain 'D' and (resid 29 through 47 )
5X-RAY DIFFRACTION5chain 'D' and (resid 48 through 60 )
6X-RAY DIFFRACTION6chain 'D' and (resid 61 through 82 )
7X-RAY DIFFRACTION7chain 'D' and (resid 83 through 97 )
8X-RAY DIFFRACTION8chain 'D' and (resid 98 through 103 )
9X-RAY DIFFRACTION9chain 'D' and (resid 104 through 109 )
10X-RAY DIFFRACTION10chain 'D' and (resid 110 through 120 )
11X-RAY DIFFRACTION11chain 'D' and (resid 121 through 126 )
12X-RAY DIFFRACTION12chain 'D' and (resid 127 through 143 )
13X-RAY DIFFRACTION13chain 'D' and (resid 144 through 165 )

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