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- PDB-2dpu: Crystal structure of the replication termination protein in compl... -

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Basic information

Entry
Database: PDB / ID: 2dpu
TitleCrystal structure of the replication termination protein in complex with a pseudosymmetric 21mer B-site DNA
Components
  • 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*T)-3'
  • 5'-D(P*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3'
  • Replication termination protein
KeywordsDNA BINDING PROTEIN/DNA / protein-DNA complex / winged-helix / DNA replication / DNA BINDING PROTEIN-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 / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsVivian, J.P. / Wilce, J. / Wilce, M.C.J.
CitationJournal: to be published
Title: Crystal structure of the replication termination protein in complex with a pseudosymmetric 21mer B-site DNA
Authors: Vivian, J.P. / Wilce, J. / Wilce, M.C.J.
History
DepositionMay 15, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 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 1.5May 29, 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(P*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3'
E: 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*T)-3'
A: Replication termination protein


Theoretical massNumber of molelcules
Total (without water)20,9223
Polymers20,9223
Non-polymers00
Water1448
1
D: 5'-D(P*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3'
E: 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*T)-3'
A: Replication termination protein

D: 5'-D(P*AP*TP*GP*TP*TP*CP*AP*TP*AP*G)-3'
E: 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*T)-3'
A: Replication termination protein


Theoretical massNumber of molelcules
Total (without water)41,8456
Polymers41,8456
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)73.049, 73.049, 68.411
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
DetailsThe asymmetric unit contains a monomer. The biological dimer is generated by the operation: rotation: -1 0 0 0-1 0 0 0 1 translation: 1 1 0

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Components

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


Mass: 3059.028 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*T)-3'


Mass: 3332.210 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Replication termination protein / Replication terminator protein


Mass: 14531.099 Da / Num. of mol.: 1 / Mutation: C110S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rtp / Plasmid: pET-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21.pLysS / References: UniProt: P68732, UniProt: P0CI76*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.75M ammonium sulfate, 0.1M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2sodium acetate11
3HOH11
4ammonium sulfate12
5sodium acetate12
6HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 5, 2000 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. all: 3829 / Num. obs: 3807 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 63 Å2
Reflection shellResolution: 3.1→3.18 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345345data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.885 / SU B: 72.99 / SU ML: 0.505 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.597 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30609 170 4.5 %RANDOM
Rwork0.20199 ---
obs0.2061 3636 99.5 %-
all-3807 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.068 Å2
Baniso -1Baniso -2Baniso -3
1--3.47 Å2-1.73 Å20 Å2
2---3.47 Å20 Å2
3---5.2 Å2
Refinement stepCycle: LAST / Resolution: 3.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 427 0 8 1396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221446
X-RAY DIFFRACTIONr_angle_refined_deg1.3692.3642025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1155114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.37124.54544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.3215209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.308155
X-RAY DIFFRACTIONr_chiral_restr0.0590.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02899
X-RAY DIFFRACTIONr_nbd_refined0.2190.2658
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2925
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.256
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.28
X-RAY DIFFRACTIONr_mcbond_it0.3041.5586
X-RAY DIFFRACTIONr_mcangle_it0.5722916
X-RAY DIFFRACTIONr_scbond_it0.7231085
X-RAY DIFFRACTIONr_scangle_it1.3144.51109
LS refinement shellResolution: 3.101→3.182 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 11 -
Rwork0.289 258 -
obs--98.9 %

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