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- PDB-1osb: Conjugative Relaxase TrwC in complex with OriT Dna. Metal-free st... -

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Basic information

Entry
Database: PDB / ID: 1osb
TitleConjugative Relaxase TrwC in complex with OriT Dna. Metal-free structure.
Components
  • Dna oligonucleotide
  • TrwC protein
KeywordsTRANSFERASE/DNA / Bacterial conjugation / Relaxase / DNA replication / TRANSFERASE-DNA COMPLEX
Function / homologyConjugative relaxase, N-terminal / TrwC relaxase / TrwC relaxase / AAA domain / P-loop containing nucleoside triphosphate hydrolase / metal ion binding / DNA / DNA (> 10) / TrwC
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGuasch, A. / Lucas, M. / Moncalian, G. / Cabezas, M. / Perez-Luque, R. / Gomis-Ruth, F.X. / de la Cruz, F. / Coll, M.
Citation
Journal: Nat.Struct.Biol. / Year: 2003
Title: Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC.
Authors: Guasch, A. / Lucas, M. / Moncalian, G. / Cabezas, M. / Perez-Luque, R. / Gomis-Ruth, F.X. / de la Cruz, F. / Coll, M.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Two active-site tyrosyl residues of protein TrwC act sequentially at the origin of transfer during plasmid R388 conjugation
Authors: Grandoso, G. / Avila, P. / Cayon, A. / Hernando, M.A. / Llosa, M. / de la Cruz, F.
#2: Journal: Mol.Microbiol. / Year: 2002
Title: Bacterial conjugation: a two-step mechanism for DNA transport.
Authors: Llosa, M. / Gomis-Ruth, F.X. / Coll, M. / de la Cruz, F.
History
DepositionMar 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 28, 2021Group: Data collection / Derived calculations / Refinement description
Category: refine / reflns ...refine / reflns / reflns_shell / struct_site
Item: _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs ..._refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_all / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 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
B: Dna oligonucleotide
D: Dna oligonucleotide
A: TrwC protein
C: TrwC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,08413
Polymers81,2204
Non-polymers8659
Water4,630257
1
B: Dna oligonucleotide
A: TrwC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0907
Polymers40,6102
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Dna oligonucleotide
C: TrwC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9946
Polymers40,6102
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.780, 147.780, 78.680
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number170
Space group name H-MP65

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Components

#1: DNA chain Dna oligonucleotide


Mass: 7714.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA forming a cruciform arm
#2: Protein TrwC protein


Mass: 32894.832 Da / Num. of mol.: 2 / Fragment: N-terminal relaxase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: Q47673
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEGMM 2000, 0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 296KK
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM ACETATE11
2AMMONIUM SULPHATE11
3SODIUM ACETATE12
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
225 %(w/v)PEG2000 MME1reservoir
30.2 Mammonium sulfate1reservoir
40.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13
DetectorType: MACSCIENCE / Detector: CCD / Date: Feb 20, 2002
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.65→40 Å / Num. obs: 28480 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 7
Reflection shellHighest resolution: 2.65 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.5 / % possible all: 97.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1OMH

1omh


Resolution: 2.65→40 Å / Cross valid method: FREE R-VALUE / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 621 2.2 %random
Rwork0.1952 ---
all0.1962 ---
obs0.1962 27852 97.3 %-
Refinement stepCycle: LAST / Resolution: 2.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4488 1012 45 257 5802
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.012
X-RAY DIFFRACTIONr_angle_refined_deg1.484
LS refinement shellResolution: 2.65→2.719 Å /
RfactorNum. reflection
Rfree0.294 47
Rwork0.221 -

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