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

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Basic information

Entry
Database: PDB / ID: 1omh
TitleConjugative Relaxase TrwC in complex with OriT Dna. Metal-free structure.
Components
  • DNA OLIGONUCLEOTIDE
  • trwC protein
KeywordsTRANSFERASE/DNA / PROTEIN-DNA COMPLEX / 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 / MAD / Resolution: 1.95 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
DepositionFeb 25, 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 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DNA OLIGONUCLEOTIDE
A: trwC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0865
Polymers40,7972
Non-polymers2883
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.830, 90.830, 203.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: DNA chain DNA OLIGONUCLEOTIDE


Mass: 7714.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA FORMING A CRUCIFORM ARM
#2: Protein trwC protein


Mass: 33082.414 Da / Num. of mol.: 1 / 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.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.3 %
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 296K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2(SO4)11
2(Na)(C2H3O2)11
3PEG11
4(Na)(C2H3O2)12
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

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9795, 0.9798, 0.9796
SYNCHROTRONESRF ID14-420.9333
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2002
RadiationMonochromator: diamond / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.97961
40.93331
ReflectionResolution: 2.05→50 Å / Num. obs: 64999 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 29.69 Å2 / Rmerge(I) obs: 0.146
Reflection shellResolution: 1.95→50 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
CNSrefinement
CCP4(SCALA)data scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→50 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2797 1851 random
Rwork0.2465 --
all0.2487 37090 -
obs0.2487 37051 -
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 512 15 256 3009
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.69249
X-RAY DIFFRACTIONc_bond_d0.005652

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