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- PDB-2dpd: Crystal structure of the Replication Termination Protein in compl... -

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Basic information

Entry
Database: PDB / ID: 2dpd
TitleCrystal structure of the Replication Termination Protein in complex with a pseudosymmetric B-site
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
KeywordsDNA BINDING PROTEIN/DNA / winged-helix protein-DNA complex / Replication Termination / Fork Arrest Mechanism / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 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 B-site
Authors: Vivian, J.P. / Wilce, J. / Wilce, M.C.J.
History
DepositionMay 9, 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 1.3Nov 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.006, 117.006, 165.553
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYSAC8 - 718 - 71
21SERSERLYSLYSBD8 - 718 - 71
32GLNGLNPHEPHEAC89 - 12289 - 122
42GLNGLNPHEPHEBD89 - 12289 - 122
DetailsThis structure represents one dimer of the functional termination complex which comprises a dimer of dimers

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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
#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
#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) / Gene: rtp / Plasmid: pET-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P68732, UniProt: P0CI76*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.86 Å3/Da / Density % sol: 68.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% MPD, 75mM sodium acetate pH 4.6, 20mM calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium acetate11
3calcium chloride11
4HOH11
5MPD12
6sodium acetate12
7calcium chloride12
8HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→60 Å / Num. all: 12241 / Num. obs: 11638 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Biso Wilson estimate: 57.1 Å2 / Rsym value: 0.069 / Net I/σ(I): 23.2
Reflection shellResolution: 3.15→3.25 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.365 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F4K with residues 71 to 89 of each monomer omitted

1f4k


Resolution: 3.17→60 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.89 / SU B: 49.763 / SU ML: 0.393 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.792 / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27781 654 5.6 %RANDOM
Rwork0.23609 ---
obs0.23835 11048 97.72 %-
all-12241 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.207 Å2
Baniso -1Baniso -2Baniso -3
1--2.87 Å2-1.44 Å20 Å2
2---2.87 Å20 Å2
3---4.31 Å2
Refinement stepCycle: LAST / Resolution: 3.17→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 855 0 12 2806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222925
X-RAY DIFFRACTIONr_angle_refined_deg1.7182.3634097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3315230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63724.38289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.02315432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0691511
X-RAY DIFFRACTIONr_chiral_restr0.0960.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021821
X-RAY DIFFRACTIONr_nbd_refined0.2440.21404
X-RAY DIFFRACTIONr_nbtor_refined0.3240.21901
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.242
Refine LS restraints NCSNumber: 823 / Type: tight positional / Rms dev position: 0.05 Å / Weight position: 0.05
LS refinement shellResolution: 3.166→3.248 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 46 -
Rwork0.29 745 -
obs--92.62 %

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