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- PDB-1zm5: Conjugative Relaxase TRWC in complex with ORIT dna, cooper-bound ... -

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Basic information

Entry
Database: PDB / ID: 1zm5
TitleConjugative Relaxase TRWC in complex with ORIT dna, cooper-bound structure
Components
  • DNA (25-MER)
  • TrwC
KeywordsDNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / BACTERIAL CONJUGATION / RELAXASE / DNA / DNA BINDING PROTEIN-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
COPPER (II) ION / DNA / DNA (> 10) / TrwC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBoer, R. / Russi, S. / Guasch, A. / Lucas, M. / Blanco, A.G. / Coll, M. / de la Cruz, F.
CitationJournal: 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.
History
DepositionMay 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (25-MER)
A: TrwC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9574
Polymers40,7972
Non-polymers1602
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.077, 91.077, 205.551
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 (25-MER)


Mass: 7714.970 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein TrwC


Mass: 33082.414 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG MME 2000, Sodium acetate, Ammonium sulfate, Cooper (II) chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG MME 200011
2Sodium acetate11
3Ammonium sulfate11
4Cooper (II) chloride11
5Sodium acetate12
6PEG MME 200012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97855 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 4, 2004 / Details: Silicon toroidal mirror coated with Rhodium
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2.5→24.68 Å / Num. all: 18254 / Num. obs: 18252 / Observed criterion σ(I): 3 / Redundancy: 21.2 % / Biso Wilson estimate: 53.8 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OMH

1omh


Resolution: 2.5→24.68 Å / Isotropic thermal model: ISOTROPIC / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.276 922 RANDOM
Rwork0.233 --
all0.261 18200 -
obs0.261 18200 -
Displacement parametersBiso mean: 37.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.116 Å2-4.397 Å20 Å2
2---4.116 Å20 Å2
3---8.231 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati sigma a0.34 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 512 7 206 3039
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.52
X-RAY DIFFRACTIONc_bond_d0.0052
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_mcbond_it1.4561.5
X-RAY DIFFRACTIONc_mcangle_it2.4842
X-RAY DIFFRACTIONc_scbond_it2.2112
X-RAY DIFFRACTIONc_scangle_it3.2462.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION43HZ.param
X-RAY DIFFRACTION5water_rep.param

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