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- PDB-2efw: Crystal structure of the RTP:nRB complex from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2efw
TitleCrystal structure of the RTP:nRB complex from Bacillus subtilis
Components
  • DNA (5'-D(*DCP*DT*DAP*DTP*DGP*DTP*DAP*DCP*DCP*DAP*DAP*DAP*DTP*DGP*DTP*DTP*DCP*DAP*DGP*DTP*DC)-3')
  • DNA (5'-D(*DGP*DAP*DCP*DTP*DGP*DAP*DAP*DCP*DAP*DTP*DTP*DTP*DGP*DGP*DTP*DAP*DCP*DAP*DTP*DAP*DG)-3')
  • Replication termination protein
KeywordsREPLICATION/DNA / protein-DNA complex / 'winged'-helix protein / DNA replication termination / replication fork arrest / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVivian, J.P. / Porter, C.J. / Wilce, J.A. / Wilce, M.C.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: An asymmetric structure of the Bacillus subtilis replication terminator protein in complex with DNA
Authors: Vivian, J.P. / Porter, C.J. / Wilce, J.A. / Wilce, M.C.J.
History
DepositionFeb 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 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 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*DCP*DT*DAP*DTP*DGP*DTP*DAP*DCP*DCP*DAP*DAP*DAP*DTP*DGP*DTP*DTP*DCP*DAP*DGP*DTP*DC)-3')
E: DNA (5'-D(*DGP*DAP*DCP*DTP*DGP*DAP*DAP*DCP*DAP*DTP*DTP*DTP*DGP*DGP*DTP*DAP*DCP*DAP*DTP*DAP*DG)-3')
I: DNA (5'-D(*DCP*DT*DAP*DTP*DGP*DTP*DAP*DCP*DCP*DAP*DAP*DAP*DTP*DGP*DTP*DTP*DCP*DAP*DGP*DTP*DC)-3')
J: DNA (5'-D(*DGP*DAP*DCP*DTP*DGP*DAP*DAP*DCP*DAP*DTP*DTP*DTP*DGP*DGP*DTP*DAP*DCP*DAP*DTP*DAP*DG)-3')
A: Replication termination protein
B: Replication termination protein
F: Replication termination protein
G: Replication termination protein


Theoretical massNumber of molelcules
Total (without water)83,8918
Polymers83,8918
Non-polymers00
Water43224
1
D: DNA (5'-D(*DCP*DT*DAP*DTP*DGP*DTP*DAP*DCP*DCP*DAP*DAP*DAP*DTP*DGP*DTP*DTP*DCP*DAP*DGP*DTP*DC)-3')
E: DNA (5'-D(*DGP*DAP*DCP*DTP*DGP*DAP*DAP*DCP*DAP*DTP*DTP*DTP*DGP*DGP*DTP*DAP*DCP*DAP*DTP*DAP*DG)-3')
A: Replication termination protein
B: Replication termination protein


Theoretical massNumber of molelcules
Total (without water)41,9464
Polymers41,9464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: DNA (5'-D(*DCP*DT*DAP*DTP*DGP*DTP*DAP*DCP*DCP*DAP*DAP*DAP*DTP*DGP*DTP*DTP*DCP*DAP*DGP*DTP*DC)-3')
J: DNA (5'-D(*DGP*DAP*DCP*DTP*DGP*DAP*DAP*DCP*DAP*DTP*DTP*DTP*DGP*DGP*DTP*DAP*DCP*DAP*DTP*DAP*DG)-3')
F: Replication termination protein
G: Replication termination protein


Theoretical massNumber of molelcules
Total (without water)41,9464
Polymers41,9464
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.012, 129.626, 125.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain DNA (5'-D(*DCP*DT*DAP*DTP*DGP*DTP*DAP*DCP*DCP*DAP*DAP*DAP*DTP*DGP*DTP*DTP*DCP*DAP*DGP*DTP*DC)-3')


Mass: 6397.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: the B site sequence of TerI
#2: DNA chain DNA (5'-D(*DGP*DAP*DCP*DTP*DGP*DAP*DAP*DCP*DAP*DTP*DTP*DTP*DGP*DGP*DTP*DAP*DCP*DAP*DTP*DAP*DG)-3')


Mass: 6486.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: the B site sequence of TerI
#3: Protein
Replication termination protein / Replication terminator protein


Mass: 14531.099 Da / Num. of mol.: 4 / Mutation: C110S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rtp / Plasmid: pET-9 / 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.: 24 / 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: 2.97 Å3/Da / Density % sol: 58.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2% PEG 4000, 125mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2sodium acetate11
3HOH11
4PEG 400012
5sodium acetate12
6HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 32161 / % possible obs: 94.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.7
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2.3 / % possible all: 84.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F4K (with residues 72 to 88 and the DNA removed)

1f4k


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.855 / SU B: 31.275 / SU ML: 0.321 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.53 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.33221 1729 5.1 %RANDOM
Rwork0.29095 ---
obs0.29303 32161 96.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.106 Å2
Baniso -1Baniso -2Baniso -3
1--4.25 Å20 Å20 Å2
2---3.33 Å20 Å2
3---7.58 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3787 1546 0 24 5357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225574
X-RAY DIFFRACTIONr_angle_refined_deg1.5322.3457786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6655448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.02524.483174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.39115842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9291520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2873
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023506
X-RAY DIFFRACTIONr_nbd_refined0.2450.21397
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22730
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.24
X-RAY DIFFRACTIONr_mcbond_it0.4081.52329
X-RAY DIFFRACTIONr_mcangle_it0.71223609
X-RAY DIFFRACTIONr_scbond_it1.04134201
X-RAY DIFFRACTIONr_scangle_it1.6944.54177
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 121 -
Rwork0.355 2275 -
obs--93.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3382-1.38910.77111.5522-0.15810.52320.11090.13360.0345-0.1176-0.09390.090.0215-0.0718-0.017-0.04350.00430.0335-0.0017-0.0004-0.128918.768324.5397120.5285
20.8728-0.2623-0.29553.22380.42562.2399-0.01120.007-0.0679-0.0750.01370.2311-0.1615-0.1844-0.00250.22960.0321-0.0944-0.10220.0069-0.3417-22.409153.319235.7942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AE8 - 1228 - 122
2X-RAY DIFFRACTION1BF8 - 1228 - 122
3X-RAY DIFFRACTION1DA3 - 213 - 21
4X-RAY DIFFRACTION1EB1 - 191 - 19
5X-RAY DIFFRACTION2FG8 - 1228 - 122
6X-RAY DIFFRACTION2GH8 - 1228 - 122
7X-RAY DIFFRACTION2IC3 - 213 - 21
8X-RAY DIFFRACTION2JD1 - 191 - 19

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