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- PDB-1j0r: Crystal structure of the replication termination protein mutant C110S -

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Basic information

Entry
Database: PDB / ID: 1j0r
TitleCrystal structure of the replication termination protein mutant C110S
Componentsreplication termination protein
KeywordsREPLICATION / winged-helix / DNA-binding protein
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
Replication termination protein / Replication termination protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVivian, J.P. / Hastings, A.F. / Duggin, I.G. / Wake, R.G. / Wilce, M.C.J. / Wilce, J.A.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2003
Title: The impact of single cysteine residue mutations on the replication terminator protein
Authors: Vivian, J.P. / Hastings, A.F. / Duggin, I.G. / Wake, R.G. / Wilce, M.C.J. / Wilce, J.A.
History
DepositionNov 20, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: replication termination protein
B: replication termination protein


Theoretical massNumber of molelcules
Total (without water)29,0622
Polymers29,0622
Non-polymers00
Water1,04558
1
A: replication termination protein

A: replication termination protein


Theoretical massNumber of molelcules
Total (without water)29,0622
Polymers29,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3080 Å2
ΔGint-26 kcal/mol
Surface area13230 Å2
MethodPISA
2
B: replication termination protein

B: replication termination protein


Theoretical massNumber of molelcules
Total (without water)29,0622
Polymers29,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3190 Å2
ΔGint-28 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.880, 50.940, 69.650
Angle α, β, γ (deg.)90.00, 91.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: 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) / Strain (production host): BL21/pLysS / References: UniProt: P68732, UniProt: P0CI76*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.45 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 22% PEG 2000, 150mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 mg/mlprotein1drop
250 mMsodium phosphate1droppH6.7
324 %PEG20001reservoir
4150 mMMES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 7, 2001 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→69 Å / Num. all: 9541 / Num. obs: 9541 / % possible obs: 88 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rsym value: 0.045
Reflection shellResolution: 2.5→2.59 Å / Rsym value: 0.471 / % possible all: 92.2
Reflection
*PLUS
% possible obs: 88 % / Num. measured all: 54110 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.66 Å / % possible obs: 92.2 % / Rmerge(I) obs: 0.471

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BM9

1bm9


Resolution: 2.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 629 Random
Rwork0.233 --
all-8327 -
obs-8327 -
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 0 58 1991
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_angle_deg1.156
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.357 77 -
Rwork0.292 --
obs-1001 92.2 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.66 Å

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