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- PDB-4xr1: Escherichia Coli Replication Terminator Protein (Tus) Complexed W... -

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Basic information

Entry
Database: PDB / ID: 4xr1
TitleEscherichia Coli Replication Terminator Protein (Tus) Complexed With DNA- AG/AT mismatch.
Components
  • DNA (5'-D(*GP*TP*AP*AP*TP*GP*TP*TP*GP*TP*AP*AP*CP*TP*A)-3')
  • DNA (5'-D(*TP*AP*GP*TP*TP*AP*CP*AP*AP*CP*AP*TP*AP*G)-3')
  • DNA replication terminus site-binding protein
KeywordsREPLICATION/DNA / DNA complex / replication / Tus / Ter / REPLICATION-DNA complex
Function / homology
Function and homology information


replication fork arrest involved in DNA replication termination / DNA replication termination / sequence-specific DNA binding / cytoplasm
Similarity search - Function
Replication Terminator Protein; Chain A, domain 2 - #10 / Replication Terminator Protein (Tus); Chain A, domain 1 / Replication terminator Tus, domain 1 superfamily/Replication terminator Tus / DNA replication terminus site-binding protein / Replication terminator Tus, domain 1 / Replication terminator Tus superfamily / DNA replication terminus site-binding protein (Ter protein) / Replication Terminator Protein; Chain A, domain 2 / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / DNA / DNA (> 10) / DNA replication terminus site-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOakley, A.J.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP0877658 Australia
Australian Research Council (ARC)DP0984797 Australia
Australian Research Council (ARC)FT0990287 Australia
CitationJournal: Nature / Year: 2015
Title: Replisome speed determines the efficiency of the Tus-Ter replication termination barrier.
Authors: Elshenawy, M.M. / Jergic, S. / Xu, Z.Q. / Sobhy, M.A. / Takahashi, M. / Oakley, A.J. / Dixon, N.E. / Hamdan, S.M.
History
DepositionJan 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: 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: DNA replication terminus site-binding protein
B: DNA (5'-D(*TP*AP*GP*TP*TP*AP*CP*AP*AP*CP*AP*TP*AP*G)-3')
C: DNA (5'-D(*GP*TP*AP*AP*TP*GP*TP*TP*GP*TP*AP*AP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,50610
Polymers46,6273
Non-polymers8807
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-54 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.811, 64.811, 246.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA replication terminus site-binding protein / Ter-binding protein


Mass: 36803.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: tus, tau, b1610, JW1602 / Plasmid: pCM862 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P16525

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*TP*AP*GP*TP*TP*AP*CP*AP*AP*CP*AP*TP*AP*G)-3')


Mass: 4896.215 Da / Num. of mol.: 1 / Mutation: C324G / Source method: obtained synthetically / Details: Ter / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(*GP*TP*AP*AP*TP*GP*TP*TP*GP*TP*AP*AP*CP*TP*A)-3')


Mass: 4927.225 Da / Num. of mol.: 1 / Mutation: A328G, G329T, T330A / Source method: obtained synthetically / Details: TerA / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 3 types, 103 molecules

#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.78 Å3/Da / Density % sol: 55.73 % / Description: bipyramids
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 8-12% (v/v) PEG 3350, 100 mM NaI, 50 mM Bis-Tris / PH range: 6.2 - 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→75 Å / Num. all: 21577 / Num. obs: 21577 / % possible obs: 99.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 24
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I06

2i06


Resolution: 2.4→62.68 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.906 / SU B: 19.482 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26899 1092 5.1 %RANDOM
Rwork0.19777 19196 --
obs0.20126 20288 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 66.995 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 2.4→62.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 574 14 96 3189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0173241
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1251.7824522
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0275312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80823.459133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.20915462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8171525
X-RAY DIFFRACTIONr_chiral_restr0.1460.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212281
X-RAY DIFFRACTIONr_gen_planes_other
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_it4.7574.1971236
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.5166.2771546
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.184.4462005
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.94637.6164846
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.402→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 86 -
Rwork0.271 1435 -
obs--99.22 %
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)
10.8548-0.1419-0.22770.8368-0.40452.722-0.0191-0.00190.12080.087-0.001-0.0905-0.04770.2180.02010.2168-0.02540.01930.2265-0.01920.0288-5.203-25.3835-15.0207
27.3054-1.0483-1.9833.7946-1.93181.9110.1404-0.3737-0.26570.11-0.2755-0.1173-0.05280.31190.1350.2713-0.0106-0.0360.2377-0.04230.0772-8.0482-27.6824-8.7791
32.98190.0479-0.95064.2558-0.22963.8405-0.059-0.2317-0.16470.15290.02730.09940.08090.02090.03170.18650.01870.03940.19690.01170.0177-8.921-28.7412-7.9565
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 1007
2X-RAY DIFFRACTION2B311 - 324
3X-RAY DIFFRACTION3C328 - 342

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