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- PDB-2i05: Escherichia Coli Replication Terminator Protein (Tus) Complexed W... -

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Basic information

Entry
Database: PDB / ID: 2i05
TitleEscherichia Coli Replication Terminator Protein (Tus) Complexed With TerA DNA
Components
  • 5'-D(*T*TP*AP*GP*TP*TP*AP*CP*AP*AP*CP*AP*TP*AP*CP*T)-3'
  • 5'-D(*TP*AP*GP*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: 2.6 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*AP*GP*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)45,8805
Polymers45,6273
Non-polymers2542
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.373, 63.373, 252.652
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*AP*GP*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 / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12.5% PEG 3350, 50mM Bis-Tris pH6.5, 200mM NaI, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2sodium iodide11
3Bis-TrisBis-tris methane11
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: 2.6→50 Å / Num. obs: 13969 / % possible obs: 82 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 5.2 % / Biso Wilson estimate: 56.028 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 28.36
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 3.1 / Num. unique all: 421 / Rsym value: 0.259 / % possible all: 25.5

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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: 2.6→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.87 / SU B: 29.777 / SU ML: 0.287 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -2 / ESU R: 1.345 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3124 690 5 %RANDOM
Rwork0.22624 ---
all0.23029 13161 --
obs0.23029 13161 82.54 %-
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: 53.288 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å20 Å20 Å2
2--2.46 Å20 Å2
3----4.93 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 608 2 10 3115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0213233
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1452.1924513
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8165304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3423.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.89415454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2591523
X-RAY DIFFRACTIONr_chiral_restr0.1170.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022261
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2630.21347
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3290.22124
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8671.51547
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57422490
X-RAY DIFFRACTIONr_scbond_it1.97732053
X-RAY DIFFRACTIONr_scangle_it3.2444.52023
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 20 -
Rwork0.338 290 -
obs--25.58 %
Refinement TLS params.Method: refined / Origin x: 38.127 Å / Origin y: 4.4711 Å / Origin z: 50.221 Å
111213212223313233
T-0.1585 Å20.0262 Å2-0.0298 Å2--0.0791 Å2-0.0506 Å2---0.0019 Å2
L0.9649 °20.517 °2-0.571 °2-1.014 °20.2471 °2--3.8445 °2
S-0.0017 Å °-0.0973 Å °-0.1342 Å °0.1175 Å °-0.0489 Å °-0.0853 Å °0.1604 Å °0.0873 Å °0.0506 Å °

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