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- PDB-6h4c: A polyamorous repressor: deciphering the evolutionary strategy us... -

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Basic information

Entry
Database: PDB / ID: 6h4c
TitleA polyamorous repressor: deciphering the evolutionary strategy used by the phage-inducible chromosomal islands to spread in nature.
Components
  • Orf20
  • dUTPaseDUTP diphosphatase
KeywordsSTRUCTURAL PROTEIN / SaPI / Repressor / Complex
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding / DNA binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / Helix-turn-helix / dUTPase-like superfamily / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. ...Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / Helix-turn-helix / dUTPase-like superfamily / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / dUTP diphosphatase / Orf20
Similarity search - Component
Biological speciesStaphylococcus phage phi11 (virus)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.52 Å
AuthorsCiges-Tomas, J.R. / Alite, C. / Bowring, J.Z. / Donderis, J. / Penades, J.R. / Marina, A.
Funding support Spain, United Kingdom, 6items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78571-P Spain
Spanish Ministry of Economy and CompetitivenessFPU13/02880 Spain
Spanish Ministry of Economy and CompetitivenessBES-2014-068617 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 670932 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: The structure of a polygamous repressor reveals how phage-inducible chromosomal islands spread in nature.
Authors: Rafael Ciges-Tomas, J. / Alite, C. / Humphrey, S. / Donderis, J. / Bowring, J. / Salvatella, X. / Penades, J.R. / Marina, A.
History
DepositionJul 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dUTPase
B: Orf20
C: dUTPase
D: Orf20
E: dUTPase
F: Orf20
G: dUTPase
H: Orf20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,50022
Polymers156,4158
Non-polymers1,08514
Water3,477193
1
A: dUTPase
B: Orf20
C: dUTPase
D: Orf20
E: dUTPase
F: Orf20
hetero molecules

A: dUTPase
B: Orf20
C: dUTPase
D: Orf20
E: dUTPase
F: Orf20
hetero molecules

A: dUTPase
B: Orf20
C: dUTPase
D: Orf20
E: dUTPase
F: Orf20
hetero molecules

G: dUTPase
H: Orf20
hetero molecules

G: dUTPase
H: Orf20
hetero molecules

G: dUTPase
H: Orf20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,49966
Polymers469,24524
Non-polymers3,25542
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-y,x-y+2,z1
crystal symmetry operation3_355-x+y-2,-x,z1
crystal symmetry operation4_368y-2,x+1,-z+31
crystal symmetry operation5_678x-y+1,-y+2,-z+31
crystal symmetry operation6_448-x-1,-x+y-1,-z+31
Buried area75970 Å2
ΔGint-320 kcal/mol
Surface area146440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.490, 144.490, 149.420
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11G-201-

MG

21G-329-

HOH

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
dUTPase / DUTP diphosphatase


Mass: 20946.338 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage phi11 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SDV3
#2: Protein
Orf20


Mass: 18157.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F0J8

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Non-polymers , 4 types, 207 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 24% PEG 1500 20% Glicerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.52→95.934 Å / Num. obs: 61269 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 55.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.052 / Rrim(I) all: 0.17 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.52-2.599.22.00344930.4770.6962.121100
11.27-64.159.10.0337750.9990.0120.03599.5

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
MOLREPphasing
RefinementResolution: 2.52→95.934 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.98
RfactorNum. reflection% reflection
Rfree0.2422 3122 5.1 %
Rwork0.1968 --
obs0.1992 61260 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.33 Å2 / Biso mean: 61.9532 Å2 / Biso min: 31.11 Å2
Refinement stepCycle: final / Resolution: 2.52→95.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9072 0 56 193 9321
Biso mean--78.83 53.25 -
Num. residues----1199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019287
X-RAY DIFFRACTIONf_angle_d1.2112628
X-RAY DIFFRACTIONf_chiral_restr0.0491456
X-RAY DIFFRACTIONf_plane_restr0.0071624
X-RAY DIFFRACTIONf_dihedral_angle_d13.9163260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5202-2.55960.34091730.276925912764
2.5596-2.60160.30831220.276426342756
2.6016-2.64640.34261390.277826012740
2.6464-2.69460.34641530.279325952748
2.6946-2.74640.30561580.263626002758
2.7464-2.80250.32531440.252726232767
2.8025-2.86340.24811330.234126142747
2.8634-2.930.3381520.225626252777
2.93-3.00330.29661260.226226222748
3.0033-3.08450.29091470.223726212768
3.0845-3.17530.33751160.223726312747
3.1753-3.27780.26731530.213626262779
3.2778-3.39490.26371320.198926472779
3.3949-3.53090.28911240.207226482772
3.5309-3.69160.26271460.19926242770
3.6916-3.88620.26431490.190426312780
3.8862-4.12970.23751550.172826342789
4.1297-4.44850.21011240.159326752799
4.4485-4.89620.17251600.145826552815
4.8962-5.60460.20911380.178626932831
5.6046-7.06090.24251380.210727092847
7.0609-96.0040.16761400.183228392979

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