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- PDB-4pcb: Conjugative Relaxase TrwC in complex with mutant OriT Dna -

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Basic information

Entry
Database: PDB / ID: 4pcb
TitleConjugative Relaxase TrwC in complex with mutant OriT Dna
Components
  • DNA 5'-D(P*GP*CP*AP*CP*CP*GP*AP*AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*CP*TP*TP*GP - 3')
  • TrwC
KeywordsTRANSFERASE/DNA / Relaxase / HUH endonuclease / plasmid conjugation / TRANSFERASE-DNA Complex
Function / homology
Function and homology information


Conjugative relaxase, N-terminal / TrwC relaxase / TrwC relaxase / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / TrwC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMoncalian, G. / Carballeira, J.D. / de la Cruz, F. / Gonzalez-Perez, B.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of EconomyBIO2008-00140 and BIO2010- 14809 Spain
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: A high security double lock and key mechanism in HUH relaxases controls oriT-processing for plasmid conjugation.
Authors: Carballeira, J.D. / Gonzalez-Perez, B. / Moncalian, G. / la Cruz, F.d.
History
DepositionApr 14, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Dec 20, 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: TrwC
B: DNA 5'-D(P*GP*CP*AP*CP*CP*GP*AP*AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*CP*TP*TP*GP - 3')
C: TrwC
D: DNA 5'-D(P*GP*CP*AP*CP*CP*GP*AP*AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*CP*TP*TP*GP - 3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1169
Polymers80,6414
Non-polymers4755
Water1,42379
1
A: TrwC
B: DNA 5'-D(P*GP*CP*AP*CP*CP*GP*AP*AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*CP*TP*TP*GP - 3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5114
Polymers40,3212
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-45 kcal/mol
Surface area16080 Å2
MethodPISA
2
C: TrwC
D: DNA 5'-D(P*GP*CP*AP*CP*CP*GP*AP*AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*CP*TP*TP*GP - 3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6065
Polymers40,3212
Non-polymers2853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-42 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.690, 148.690, 77.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein TrwC


Mass: 32894.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwC / Production host: Escherichia coli (E. coli) / References: UniProt: Q47673
#2: DNA chain DNA 5'-D(P*GP*CP*AP*CP*CP*GP*AP*AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*CP*TP*TP*GP - 3')


Mass: 7425.789 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 200 mM NaCl, 20 mM TrisHCl [pH 7.5], 1 mM dithiothreitol [DTT], 0.5 mM ethylenediaminetetraacetic acid [EDTA]

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.45→66.6 Å / Num. obs: 36116 / % possible obs: 98.8 % / Redundancy: 9.4 % / Net I/σ(I): 15.5
Reflection shellResolution: 2.45→2.57 Å / % possible obs: 99.8 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.124

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OMH

1omh


Resolution: 2.5→66.596 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 39.27 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2944 1699 5 %
Rwork0.2551 --
obs0.2572 33996 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→66.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4426 906 25 79 5436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115516
X-RAY DIFFRACTIONf_angle_d1.4477597
X-RAY DIFFRACTIONf_dihedral_angle_d20.3072136
X-RAY DIFFRACTIONf_chiral_restr0.063827
X-RAY DIFFRACTIONf_plane_restr0.008833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.57350.33591330.29492671X-RAY DIFFRACTION95
2.5735-2.65660.34821390.29482680X-RAY DIFFRACTION95
2.6566-2.75140.35141350.28362656X-RAY DIFFRACTION95
2.7514-2.86150.36171350.2922674X-RAY DIFFRACTION95
2.8615-2.99160.34321390.28112681X-RAY DIFFRACTION95
2.9916-3.14920.36041360.28312670X-RAY DIFFRACTION95
3.1492-3.34620.29671620.27332673X-RAY DIFFRACTION94
3.3462-3.60420.32781420.2482681X-RAY DIFFRACTION95
3.6042-3.96610.28141490.24152685X-RAY DIFFRACTION95
3.9661-4.53830.25041310.22492737X-RAY DIFFRACTION95
4.5383-5.7110.22831510.22412700X-RAY DIFFRACTION95
5.711-29.54380.23271450.23882776X-RAY DIFFRACTION95

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