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

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Basic information

Entry
Database: PDB / ID: 5myd
TitleConvergent evolution involving dimeric and trimeric dUTPases in signalling.
ComponentsDUTPase
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 / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / dUTPase
Function and homology information
Biological speciesStaphylococcus sp. HMSC068C09 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsDonderis, J. / Bowring, J. / Maiques, E. / Ciges-Tomas, J.R. / Alite, C. / Mehmedov, I. / Tormo-Mas, M.A. / Penades, J.R. / Marina, A.
Funding support Spain, United Kingdom, 6items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2013-42619-P Spain
Spanish Ministry of Economy and CompetitivenessBIO2016-78571-P Spain
Valencian GovernmentPrometeo II/2014/029 Spain
Medical Research Council (United Kingdom)MR/M003876/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N002873/1 United Kingdom
European Research CouncilERC-ADG-2014
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUTPase
B: DUTPase
C: DUTPase
D: DUTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,68716
Polymers96,6244
Non-polymers2,06312
Water3,783210
1
A: DUTPase
hetero molecules

C: DUTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3448
Polymers48,3122
Non-polymers1,0326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
MethodPISA
2
C: DUTPase
hetero molecules

A: DUTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3448
Polymers48,3122
Non-polymers1,0326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
MethodPISA
3
B: DUTPase
hetero molecules

D: DUTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3448
Polymers48,3122
Non-polymers1,0326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
MethodPISA
4
D: DUTPase
hetero molecules

B: DUTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3448
Polymers48,3122
Non-polymers1,0326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.890, 81.440, 81.530
Angle α, β, γ (deg.)90.00, 106.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRHISHISAA2 - 15936 - 193
21THRTHRHISHISBB2 - 15936 - 193
12METMETHISHISAA1 - 15935 - 193
22METMETHISHISCC1 - 15935 - 193
13THRTHRHISHISAA2 - 15936 - 193
23THRTHRHISHISDD2 - 15936 - 193
14THRTHRASPASPBB2 - 16336 - 197
24THRTHRASPASPCC2 - 16336 - 197
15THRTHRGLNGLNBB2 - 16236 - 196
25THRTHRGLNGLNDD2 - 16236 - 196
16THRTHRGLNGLNCC2 - 16236 - 196
26THRTHRGLNGLNDD2 - 16236 - 196

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
DUTPase


Mass: 24156.105 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus sp. HMSC068C09 (bacteria)
Gene: HMPREF2930_08375 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2D0TC86*PLUS, dUTP diphosphatase
#2: Chemical
ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6753.98
2
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8% PEG 3350, 0.1 M Na-HEPES pH 7.5; 0.2M NaCl, 1.2 M ammonium sulphate and 0.03 M ammonium acetate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0410.97942
SYNCHROTRONALBA XALOC20.97925
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELJul 1, 2013
DECTRIS PILATUS3 6M2PIXEL
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.979251
Reflection

Entry-ID: 5MYD

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.1-81.445073699.2440.04818.4
3-81.231794599.970.0642
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obs% possible allNum. unique all
2.1-2.213.70.352.1732598.9
3-3.167.20.4599.92608

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→78.12 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.895 / SU B: 19.115 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.246 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26533 1962 5.1 %RANDOM
Rwork0.22376 ---
obs0.22589 36770 99.21 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 47.915 Å2
Baniso -1Baniso -2Baniso -3
1-3.66 Å20 Å21.07 Å2
2---3.44 Å20 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 2.3→78.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5375 0 120 210 5705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025623
X-RAY DIFFRACTIONr_bond_other_d0.0060.025098
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.987634
X-RAY DIFFRACTIONr_angle_other_deg1.344311704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1975648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85425.275309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72615959
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8171524
X-RAY DIFFRACTIONr_chiral_restr0.0790.2821
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026340
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021348
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_it3.0361.9132598
X-RAY DIFFRACTIONr_mcbond_other3.0351.9122597
X-RAY DIFFRACTIONr_mcangle_it4.2032.8623241
X-RAY DIFFRACTIONr_mcangle_other4.2032.8643242
X-RAY DIFFRACTIONr_scbond_it4.9462.3833025
X-RAY DIFFRACTIONr_scbond_other4.9422.3823024
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9473.4774393
X-RAY DIFFRACTIONr_long_range_B_refined8.44916.7696568
X-RAY DIFFRACTIONr_long_range_B_other8.44516.5846536
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A194320.09
12B194320.09
21A192680.09
22C192680.09
31A192600.1
32D192600.1
41B199740.07
42C199740.07
51B197340.09
52D197340.09
61C197420.08
62D197420.08
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 135 -
Rwork0.273 2708 -
obs--99.16 %
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)
12.6872-0.27110.7362.14590.50362.6755-0.0304-0.00920.0538-0.1611-0.17550.2416-0.0498-0.40270.20590.08680.0456-0.08020.5334-0.05010.14044.84865.88330.968
22.5747-0.1913-0.22182.2964-0.84722.31730.0569-0.1022-0.03190.0071-0.1149-0.3227-0.1070.23990.0580.0182-0.0181-0.04490.54960.01610.2248-16.20854.7123.493
32.42660.25720.62571.6758-0.42052.9195-0.0819-0.0230.04480.0994-0.04780.0378-0.0352-0.1620.12970.0192-0.0164-0.03170.45350.00950.13122.10629.57527.644
43.536-0.6856-0.22192.0683-0.44591.94120.02470.2312-0.02120.0482-0.02690.1362-0.092-0.17390.00220.0193-0.0038-0.03530.48560.01270.10726.36552.2267.596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 160
2X-RAY DIFFRACTION2B2 - 164
3X-RAY DIFFRACTION3C1 - 164
4X-RAY DIFFRACTION4D2 - 163

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