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- PDB-5vfy: Structure of an accessory protein of the pCW3 relaxosome -

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Basic information

Entry
Database: PDB / ID: 5vfy
TitleStructure of an accessory protein of the pCW3 relaxosome
ComponentsTcpK
KeywordsDNA BINDING PROTEIN / conjugation / winged helix-turn-helix / clostridium perfringens
Function / homologyCch, helix turn helix domain / Cch helix turn helix domain / Cch helix turn helix domain-containing protein
Function and homology information
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 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 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TcpK
B: TcpK
C: TcpK
D: TcpK


Theoretical massNumber of molelcules
Total (without water)52,0204
Polymers52,0204
Non-polymers00
Water3,369187
1
A: TcpK
B: TcpK


Theoretical massNumber of molelcules
Total (without water)26,0102
Polymers26,0102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-9 kcal/mol
Surface area11060 Å2
MethodPISA
2
C: TcpK
D: TcpK


Theoretical massNumber of molelcules
Total (without water)26,0102
Polymers26,0102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-12 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.560, 120.590, 52.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
TcpK


Mass: 13005.041 Da / Num. of mol.: 4
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 / References: UniProt: Q1PLI2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 50.72 % / Mosaicity: 0.29 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1 M Na Citrate, 0.1 M Na Cacodylate, 0.1M Phenol

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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: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.49→48.44 Å / Num. obs: 18698 / % possible obs: 99.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 29.75 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.088 / Rrim(I) all: 0.232 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.49-2.595.90.8690.6850.3730.95197.2
8.97-48.445.30.0910.9860.0430.10193.6

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.49→44.21 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.855 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.485 / SU Rfree Blow DPI: 0.259 / SU Rfree Cruickshank DPI: 0.255
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1099 5.9 %RANDOM
Rwork0.181 ---
obs0.184 18625 99.6 %-
Displacement parametersBiso max: 123.97 Å2 / Biso mean: 27.58 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-3.8366 Å20 Å20 Å2
2--10.3122 Å20 Å2
3----14.1488 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.49→44.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3410 0 0 187 3597
Biso mean---34.57 -
Num. residues----409
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1273SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes485HARMONIC5
X-RAY DIFFRACTIONt_it3491HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion436SEMIHARMONIC5
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_contact3936SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3491HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4701HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion19.34
LS refinement shellResolution: 2.49→2.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.258 172 5.84 %
Rwork0.209 2771 -
all0.211 2943 -
obs--99.06 %

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