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- PDB-1f4k: CRYSTAL STRUCTURE OF THE REPLICATION TERMINATOR PROTEIN/B-SITE DN... -

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Basic information

Entry
Database: PDB / ID: 1f4k
TitleCRYSTAL STRUCTURE OF THE REPLICATION TERMINATOR PROTEIN/B-SITE DNA COMPLEX
Components
  • 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*AP*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3'
  • 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*TP*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3'
  • REPLICATION TERMINATION PROTEIN
KeywordsREPLICATION/DNA / winged-helix protein-DNA complex / REPLICATION AND TERMINATION / FORK ARREST MECHANISM / REPLICATION-DNA COMPLEX
Function / homology
Function and homology information


DNA replication termination / DNA binding
Similarity search - Function
Replication terminator protein / Replication terminator protein / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Replication termination protein / Replication termination protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsWilce, J.A. / Vivian, J.P. / Hastings, A.F. / Otting, G. / Folmer, R.H.A. / Duggin, I.G. / Wake, R.G. / Wilce, M.C.J.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of the RTP-DNA complex and the mechanism of polar replication fork arrest
Authors: Wilce, J.A. / Vivian, J.P. / Hastings, A.F. / Otting, G. / Folmer, R.H. / Duggin, I.G. / Wake, R.G. / Wilce, M.C.
History
DepositionJun 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*AP*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3'
E: 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*TP*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3'
A: REPLICATION TERMINATION PROTEIN
B: REPLICATION TERMINATION PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,9444
Polymers41,9444
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.780, 44.780, 395.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221
DetailsThe whole biological assembly is contained in the asymmetric unit. It comprises a homodimer constructed from chain A and B bound to double stranded DNA (chains D and E).

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Components

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


Mass: 6445.209 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: PSEUDOSYMMETRIC B-SITE OF THE TERI SEQUENCE OF B. SUBTILIS
#2: DNA chain 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*TP*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3'


Mass: 6436.195 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: PSEUDOSYMMETRIC B-SITE OF THE TERI SEQUENCE OF B. SUBTILIS
#3: Protein REPLICATION TERMINATION PROTEIN / REPLICATION TERMINATOR PROTEIN


Mass: 14531.099 Da / Num. of mol.: 2 / Mutation: C110S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PET-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P68732, UniProt: P0CI76*PLUS
#4: 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: 2.94 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 5% PEG 4000, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium acetate11
2PEG 400011
3PEG 400012
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-7 %(w/v)PEG40001reservoir
20.075-0.100 Msodium acetate1reservoir
31

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 15166 / % possible obs: 87.9 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 60.5 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.7
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.175 / % possible all: 54.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 15166 / Num. measured all: 147110
Reflection shell
*PLUS
% possible obs: 54.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: protein_rep.param, dna-rna_rep.param, water_rep.param
RfactorNum. reflection% reflectionSelection details
Rfree0.2759 1509 10 %random
Rwork0.2279 ---
all0.271 15166 --
obs0.271 15166 87.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.784 Å2-6.708 Å20 Å2
2---7.784 Å20 Å2
3---15.569 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 855 0 96 2873
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009658
X-RAY DIFFRACTIONc_angle_deg1.72021
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / Rfactor Rfree: 0.381 / Rfactor obs: 0.301

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