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- PDB-1ecr: ESCHERICHIA COLI REPLICATION TERMINATOR PROTEIN (TUS) COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 1ecr
TitleESCHERICHIA COLI REPLICATION TERMINATOR PROTEIN (TUS) COMPLEXED WITH DNA
Components
  • DNA (5'-D(*TP*AP*GP*TP*AP*TP*GP*TP*TP*GP*TP*AP*AP*CP*TP*A)-3
  • DNA (5'-D(*TP*TP*AP*GP*TP*TP*AP*CP*AP*AP*CP*AP*TP*AP*CP*T)-3
  • PROTEIN (REPLICATION-TERMINATOR PROTEIN)
KeywordsREPLICATION/DNA / DNA-BINDING / DNA REPLICATION / COMPLEX (DNA-BINDING PROTEIN-DNA) / 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
DNA / DNA (> 10) / DNA replication terminus site-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, ANOMALOUS SCATTERING / Resolution: 2.7 Å
AuthorsKamada, K. / Morikawa, K.
Citation
Journal: Nature / Year: 1996
Title: Structure of a replication-terminator protein complexed with DNA.
Authors: Kamada, K. / Horiuchi, T. / Ohsumi, K. / Shimamoto, N. / Morikawa, K.
#1: Journal: Proteins / Year: 1996
Title: Crystallization and Preliminary X-Ray Analysis of the Escherichia Coli Replication Terminator Protein Complexed with DNA
Authors: Kamada, K. / Ohsumi, K. / Horiuchi, T. / Shimamoto, N. / Morikawa, K.
History
DepositionSep 1, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 5, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: DNA (5'-D(*TP*TP*AP*GP*TP*TP*AP*CP*AP*AP*CP*AP*TP*AP*CP*T)-3
C: DNA (5'-D(*TP*AP*GP*TP*AP*TP*GP*TP*TP*GP*TP*AP*AP*CP*TP*A)-3
A: PROTEIN (REPLICATION-TERMINATOR PROTEIN)


Theoretical massNumber of molelcules
Total (without water)45,6273
Polymers45,6273
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.150, 68.150, 230.720
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 DNA (5'-D(*TP*TP*AP*GP*TP*TP*AP*CP*AP*AP*CP*AP*TP*AP*CP*T)-3 / TER


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


Mass: 4927.225 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (REPLICATION-TERMINATOR PROTEIN) / TUS


Mass: 35843.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / Plasmid: PHO100 / Gene (production host): TUS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P16525
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 5.3 / Details: pH 5.30, MICRODIALYSIS, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 400011
3WATER12
4PEG 400012
5NA CITRATE12
6NACL12
7GLYCEROL12
8SPERMINE12
9EDTA12
10DTT12
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.3
Details: Kamada, K., (1996) Proteins: Struct.,Funct., Genet., 24, 402.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formula
10.25 mMprotein1
20.35 mMDNA duplex1
350 mMNa citrate1
4100 mM1NaCl
510 %(v/v)glycerol1
62 mMspermine1
71 mMEDTA1
81 mMDTT1
910 %(w/v)PEG40001
101

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 13, 1994 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 14018 / % possible obs: 90.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rsym value: 0.06
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.6 % / Rsym value: 0.217 / % possible all: 75.1
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 50 Å / % possible obs: 90.4 % / Rmerge(I) obs: 0.06

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Processing

Software
NameClassification
CCP4model building
X-PLORrefinement
MACDENZOdata reduction
MACDENZOdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR, ANOMALOUS SCATTERING / Resolution: 2.7→10 Å / σ(F): 0
RfactorNum. reflection
Rfree0.314 -
Rwork0.196 -
obs0.196 12726
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 608 0 49 3152
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 10 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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