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- PDB-2i06: Escherichia Coli Replication Terminator Protein (Tus) Complexed W... -

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Basic information

Entry
Database: PDB / ID: 2i06
TitleEscherichia Coli Replication Terminator Protein (Tus) Complexed With DNA- Locked form
Components
  • 5'-D(*T*TP*AP*GP*TP*TP*AP*CP*AP*AP*CP*AP*TP*AP*CP*T)-3'
  • 5'-D(*TP*G*AP*TP*AP*TP*GP*TP*TP*GP*TP*AP*AP*CP*TP*A)-3'
  • DNA replication terminus site-binding protein
KeywordsREPLICATION/DNA / PROTEIN-DNA COMPLEX / 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: 2.2 Å
AuthorsOakley, A.J. / Mulcair, M.D. / Schaeffer, P.M. / Dixon, N.E.
Citation
Journal: To be Published
Title: Polarity of Termination of DNA Replication in E. coli.
Authors: Oakley, A.J. / Mulcair, M.D. / Schaeffer, P.M. / Dixon, N.E.
#1: Journal: CELL(CAMBRIDGE,MASS.) / Year: 2006
Title: A molecular mousetrap determines polarity of termination of DNA replication in E. coli
Authors: Mulcair, M.D. / Schaeffer, P.M. / Oakley, A.J. / Cross, H.F. / Neylon, C. / Hill, T.M. / Dixon, N.E.
History
DepositionAug 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*T*TP*AP*GP*TP*TP*AP*CP*AP*AP*CP*AP*TP*AP*CP*T)-3'
C: 5'-D(*TP*G*AP*TP*AP*TP*GP*TP*TP*GP*TP*AP*AP*CP*TP*A)-3'
A: DNA replication terminus site-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0076
Polymers45,6273
Non-polymers3813
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.834, 62.834, 252.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: DNA chain 5'-D(*T*TP*AP*GP*TP*TP*AP*CP*AP*AP*CP*AP*TP*AP*CP*T)-3'


Mass: 4856.191 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*G*AP*TP*AP*TP*GP*TP*TP*GP*TP*AP*AP*CP*TP*A)-3'


Mass: 4927.225 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA replication terminus site-binding protein / Ter-binding protein


Mass: 35843.188 Da / Num. of mol.: 1 / Fragment: TUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tus / Plasmid: pCM847 / Production host: Escherichia coli (E. coli) / Strain (production host): AN1459 / References: UniProt: P16525
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 13% PEG 3350, 50mM Bis-Tris pH6.75, 200mM NaI, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2sodium iodide11
3Bis-Tris11
4water11
5PEG 335012
6sodium iodide12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2006
Details: Rosenbaum-Rock monochromator, high-resolution double-crystal sagittal focusing, double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 17442 / % possible obs: 64.6 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 5.1 % / Biso Wilson estimate: 26.833 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 25.52
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 4.04 / Num. unique all: 344 / Rsym value: 0.175 / % possible all: 13.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EWJ

2ewj


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / SU B: 25.679 / SU ML: 0.262 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -2 / ESU R: 0.492 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The crystals gave anisotropic diffraction, with stronger diffraction along c* than a*/b*. Thus completeness tends to fall off toward the high-resolution end.
RfactorNum. reflection% reflectionSelection details
Rfree0.28032 878 5.1 %RANDOM
Rwork0.2178 ---
all0.22098 16499 --
obs0.22098 16499 64.84 %-
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: 62.881 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å20 Å20 Å2
2--2.22 Å20 Å2
3----4.44 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 537 3 71 3106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213152
X-RAY DIFFRACTIONr_angle_refined_deg1.962.174390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1385304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89523.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.46115454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9221523
X-RAY DIFFRACTIONr_chiral_restr0.1090.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022218
X-RAY DIFFRACTIONr_nbd_refined0.230.21263
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21975
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2129
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4050.23
X-RAY DIFFRACTIONr_mcbond_it0.7921.51541
X-RAY DIFFRACTIONr_mcangle_it1.45922490
X-RAY DIFFRACTIONr_scbond_it1.98931932
X-RAY DIFFRACTIONr_scangle_it3.1914.51900
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.796 11 -
Rwork0.434 222 -
obs--12.05 %
Refinement TLS params.Method: refined / Origin x: 37.5427 Å / Origin y: 4.8955 Å / Origin z: 49.8063 Å
111213212223313233
T-0.1689 Å2-0.0164 Å20.0134 Å2--0.1437 Å2-0.029 Å2---0.0691 Å2
L1.076 °20.2729 °2-0.3865 °2-0.8801 °20.2461 °2--3.3166 °2
S0.0043 Å °-0.0764 Å °-0.1061 Å °0.1219 Å °-0.0772 Å °-0.016 Å °0.1686 Å °0.0444 Å °0.0729 Å °

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