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- PDB-2cdm: The structure of TrwC complexed with a 27-mer DNA comprising the ... -

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Basic information

Entry
Database: PDB / ID: 2cdm
TitleThe structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site
Components
  • 5'-D(*GP*CP*GP*CP*AP*CP*CP*GP*AP*AP *AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*GP*TP*CP*TP*AP*T)-3'
  • TRWC
KeywordsDNA/DNA-BINDING PROTEIN / RELAXASE / BACTERIAL CONJUGATION / DNA TRANSFER / DNA-PROTEIN COMPLEX / DNA-DNA-BINDING PROTEIN 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: 2.7 Å
AuthorsBoer, R. / Russi, S. / Guasch, A. / Lucas, M. / Blanco, A.G. / Perez-Luque, R. / Coll, M. / de la Cruz, F.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Unveiling the Molecular Mechanism of a Conjugative Relaxase: The Structure of Trwc Complexed with a 27-mer DNA Comprising the Recognition Hairpin and the Cleavage Site.
Authors: Boer, R. / Russi, S. / Guasch, A. / Lucas, M. / Blanco, A.G. / Perez-Luque, R. / Coll, M. / De La Cruz, F.
#1: 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.
History
DepositionJan 25, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRWC
B: 5'-D(*GP*CP*GP*CP*AP*CP*CP*GP*AP*AP *AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*GP*TP*CP*TP*AP*T)-3'
C: TRWC
D: 5'-D(*GP*CP*GP*CP*AP*CP*CP*GP*AP*AP *AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*GP*TP*CP*TP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9906
Polymers82,7984
Non-polymers1922
Water4,270237
1
A: TRWC
B: 5'-D(*GP*CP*GP*CP*AP*CP*CP*GP*AP*AP *AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*GP*TP*CP*TP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4953
Polymers41,3992
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: TRWC
D: 5'-D(*GP*CP*GP*CP*AP*CP*CP*GP*AP*AP *AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*GP*TP*CP*TP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4953
Polymers41,3992
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)148.383, 148.383, 79.505
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: 33066.414 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-293 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SELENO METHIONINE DERIVATIVE / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Description: FROM THE PLASMID R388 / Plasmid: PSU1621 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q47673
#2: DNA chain 5'-D(*GP*CP*GP*CP*AP*CP*CP*GP*AP*AP *AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*GP*TP*CP*TP*AP*T)-3' / ORIT


Mass: 8332.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: FROM THE PLASMID R388 / Source: (synth.) ESCHERICHIA COLI (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 18 TO PHE ENGINEERED RESIDUE IN CHAIN C, TYR 18 TO PHE
Has protein modificationY
Sequence detailsRESIDUES 1-293 T27 DISORDERED AND NOT MODELLED

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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: 3.2 Å3/Da / Density % sol: 51.5 %
Crystal growpH: 4.6
Details: 32 % PEG MME 2000, 0.3 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979269
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 26, 2004 / Details: CRYSTALS AND MIRRORS
RadiationMonochromator: DIAMOND CRYSTAL (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979269 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 27451 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.6
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OSB

1osb


Resolution: 2.7→25 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.897 / SU B: 10.49 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.72 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1377 5 %RANDOM
Rwork0.205 ---
obs0.207 26050 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.14 Å20 Å2
2--0.27 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4426 971 10 237 5644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215582
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3652.1777709
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8845556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48923.246228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94515842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.991552
X-RAY DIFFRACTIONr_chiral_restr0.1020.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023877
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.22270
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23634
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.2105
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7281.52838
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33524378
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.42133391
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.624.53331
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 104
Rwork0.266 1866

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