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

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Basic information

Entry
Database: PDB / ID: 2ewj
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 / Tus / terminus site / protein-DNA interaction / replication arrest / 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOakley, A.J. / Mulcair, M.D. / Schaeffer, P.M. / Dixon, N.E.
CitationJournal: 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
DepositionNov 3, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 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
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.679, 62.679, 251.619
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 protein / Ter binding protein


Mass: 35843.188 Da / Num. of mol.: 1 / Fragment: Termination Utilization Substance
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tus / Production host: Escherichia coli (E. coli) / 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.: 27 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 13% PEG 3350, 0.2M sodium iodide, 50mM Bis-Tris pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2sodium iodide11
3water11
4PEG 335012
5sodium iodide12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 18, 2005 / Details: Osmic blue mirrors
RadiationMonochromator: Osmic blue mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 14359 / % possible obs: 97.9 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Rmerge(I) obs: 0.112 / Net I/σ(I): 9.3
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 1.9 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ECR

1ecr


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.866 / SU B: 14.847 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.921 / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3026 716 5 %RANDOM
Rwork0.21851 ---
all0.22259 14287 --
obs0.22259 13571 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.963 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å20 Å20 Å2
2--2.32 Å20 Å2
3----4.65 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 537 3 27 3062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213152
X-RAY DIFFRACTIONr_angle_refined_deg2.0672.1634389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4115304
X-RAY DIFFRACTIONr_chiral_restr0.1220.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022218
X-RAY DIFFRACTIONr_nbd_refined0.2490.21275
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.297
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.24
X-RAY DIFFRACTIONr_mcbond_it0.9091.51534
X-RAY DIFFRACTIONr_mcangle_it1.70722489
X-RAY DIFFRACTIONr_scbond_it2.19431618
X-RAY DIFFRACTIONr_scangle_it3.5184.51900
LS refinement shellResolution: 2.705→2.775 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.437 45
Rwork0.322 983
Refinement TLS params.Method: refined / Origin x: 37.417 Å / Origin y: 4.7497 Å / Origin z: 49.7285 Å
111213212223313233
T0.0154 Å2-0.0165 Å20.0126 Å2-0.0227 Å2-0.0259 Å2--0.0408 Å2
L0.1451 °2-0.0365 °2-0.1971 °2-0.1614 °20.0938 °2--1.4689 °2
S-0.015 Å °0.0002 Å °-0.0252 Å °0.0303 Å °-0.034 Å °-0.0048 Å °0.0888 Å °0.0113 Å °0.049 Å °

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