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- PDB-2dqr: Crystal structure of the replication terminator protein mutant RT... -

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Basic information

Entry
Database: PDB / ID: 2dqr
TitleCrystal structure of the replication terminator protein mutant RTP.E39K.R42Q
ComponentsReplication termination protein
KeywordsDNA BINDING PROTEIN / DNA replication / winged-helix / RTP
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: 3.01 Å
AuthorsVivian, J.P. / Wilce, J.A. / Wilce, M.C.J.
CitationJournal: to be published
Title: Crystal structure of the replication terminator protein mutant RTP.E39K.R42Q
Authors: Vivian, J.P. / Wilce, J.A. / Wilce, M.C.J.
History
DepositionMay 29, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 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 1.5Apr 3, 2024Group: 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
C: Replication termination protein
D: Replication termination protein


Theoretical massNumber of molelcules
Total (without water)58,0734
Polymers58,0734
Non-polymers00
Water1,820101
1
A: Replication termination protein
B: Replication termination protein


Theoretical massNumber of molelcules
Total (without water)29,0362
Polymers29,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-27 kcal/mol
Surface area11920 Å2
MethodPISA
2
C: Replication termination protein
D: Replication termination protein


Theoretical massNumber of molelcules
Total (without water)29,0362
Polymers29,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-25 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.922, 72.805, 195.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains two dimers. The biological unit is one dimer.

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Components

#1: Protein
Replication termination protein / Replication terminator protein


Mass: 14518.165 Da / Num. of mol.: 4 / Mutation: E39K,R42Q
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% PEG 4000, 0.2M sodium acetate, 0.225M Tris HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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: May 5, 2002 / 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→90 Å / Num. all: 12062 / Num. obs: 12062 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.142
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.69 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345mar345data collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bm9_A (residues 72 to 88 omitted)

Resolution: 3.01→25.45 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.87 / SU B: 38.83 / SU ML: 0.348 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27626 575 4.8 %RANDOM
Rwork0.20162 ---
obs0.20532 11485 98.84 %-
all-11485 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.157 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 3.01→25.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 0 101 3749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223700
X-RAY DIFFRACTIONr_angle_refined_deg1.572.0034931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8695426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16324.675169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.75815809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6271517
X-RAY DIFFRACTIONr_chiral_restr0.1080.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022613
X-RAY DIFFRACTIONr_nbd_refined0.2450.21840
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3240.27
X-RAY DIFFRACTIONr_mcbond_it0.5131.52248
X-RAY DIFFRACTIONr_mcangle_it0.89923466
X-RAY DIFFRACTIONr_scbond_it1.24231658
X-RAY DIFFRACTIONr_scangle_it2.0574.51465
LS refinement shellResolution: 3.01→3.087 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 34 -
Rwork0.336 799 -
obs--95.2 %

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