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- PDB-5vfx: Structure of an accessory protein of the pCW3 relaxosome in compl... -

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Basic information

Entry
Database: PDB / ID: 5vfx
TitleStructure of an accessory protein of the pCW3 relaxosome in complex with the origin of transfer (oriT) DNA
Components
  • (oriT) x 2
  • TcpK
KeywordsDNA BINDING PROTEIN/DNA / conjugation / winged helix-turn-helix / oriT / clostridium perfringens / DNA BINDING PROTEIN-DNA complex
Function / homologyCch helix turn helix domain / DNA / DNA (> 10) / Uncharacterized protein
Function and homology information
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsTraore, D.A.K. / Wisniewski, J.A. / Flanigan, S.F. / Conroy, P.J. / Panjikar, S. / Mok, Y.-F. / Lao, C. / Griffin, M.D.W. / Adams, V. / Rood, J.I. / Whisstock, J.C.
CitationJournal: Nat Commun / Year: 2018
Title: Crystal structure of TcpK in complex with oriT DNA of the antibiotic resistance plasmid pCW3.
Authors: Traore, D.A.K. / Wisniewski, J.A. / Flanigan, S.F. / Conroy, P.J. / Panjikar, S. / Mok, Y.F. / Lao, C. / Griffin, M.D.W. / Adams, V. / Rood, J.I. / Whisstock, J.C.
History
DepositionApr 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TcpK
B: TcpK
C: TcpK
D: TcpK
E: TcpK
F: TcpK
G: TcpK
H: TcpK
I: oriT
J: oriT
K: oriT
L: oriT
M: oriT
N: oriT
O: oriT
P: oriT


Theoretical massNumber of molelcules
Total (without water)160,51316
Polymers160,51316
Non-polymers00
Water48627
1
A: TcpK
B: TcpK
C: TcpK
D: TcpK
I: oriT
J: oriT
K: oriT
L: oriT


Theoretical massNumber of molelcules
Total (without water)80,2578
Polymers80,2578
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14570 Å2
ΔGint-74 kcal/mol
Surface area32290 Å2
MethodPISA
2
E: TcpK
F: TcpK
G: TcpK
H: TcpK
M: oriT
N: oriT
O: oriT
P: oriT


Theoretical massNumber of molelcules
Total (without water)80,2578
Polymers80,2578
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13770 Å2
ΔGint-80 kcal/mol
Surface area32500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.503, 109.894, 122.780
Angle α, β, γ (deg.)90.000, 93.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TcpK


Mass: 13005.041 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria)
Gene: ERS852446_03033, pBeta2_00022, pCpb2-CP1_20, pCW3_0028, pNetB-NE10_20, pNetB_00021, pTet_021
Plasmid: pGL12 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q1PLI2
#2: DNA chain
oriT


Mass: 7112.636 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Clostridium perfringens (bacteria)
#3: DNA chain
oriT


Mass: 7005.545 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Clostridium perfringens (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.92 Å3/Da / Density % sol: 57.84 % / Mosaicity: 0.24 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M imidazole, 50% (v/v) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.81→47.2 Å / Num. obs: 44405 / % possible obs: 98.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 81.15 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.098 / Rrim(I) all: 0.192 / Net I/σ(I): 6.5 / Num. measured all: 166112 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.81-2.913.62.11585244310.2171.2642.4580.793.6
10.5-47.23.70.03431448480.9980.020.042594.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VFY

5vfy


Resolution: 2.81→43.08 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.97 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.867 / SU Rfree Blow DPI: 0.307 / SU Rfree Cruickshank DPI: 0.313
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2236 5.04 %RANDOM
Rwork0.198 ---
obs0.2 44345 98.5 %-
Displacement parametersBiso max: 151.84 Å2 / Biso mean: 67.63 Å2 / Biso min: 23.33 Å2
Baniso -1Baniso -2Baniso -3
1--3.3356 Å20 Å219.3939 Å2
2--5.9744 Å20 Å2
3----2.6387 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: final / Resolution: 2.81→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6472 3752 0 27 10251
Biso mean---41.98 -
Num. residues----983
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3229SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes160HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1125HARMONIC5
X-RAY DIFFRACTIONt_it10794HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1403SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11024SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10794HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg15379HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion23.94
LS refinement shellResolution: 2.81→2.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 184 5.7 %
Rwork0.245 3046 -
all0.247 3230 -
obs--96.8 %

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