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- PDB-1qx0: CONJUGATIVE RELAXASE TRWC IN COMPLEX WITH ORIT DNA. METAL-BOUND S... -

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Open data

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Basic information

Entry

Database: PDB / ID: 1qx0

Title

CONJUGATIVE RELAXASE TRWC IN COMPLEX WITH ORIT DNA. METAL-BOUND STRUCTURE

Components

DNA OLIGONUCLEOTIDE
trwC protein

Keywords

TRANSFERASE/DNA / PROTEIN-DNA COMPLEX / BACTERIAL CONJUGATION / RELAXASE / DNA REPLICATION / TRANSFERASE-DNA COMPLEX

Function / homology

Function and homology information

G-quadruplex DNA unwinding / mitochondrial genome maintenance / replication fork reversal / telomere maintenance / single-stranded DNA binding / metal ion binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.26 Å

Authors

Guasch, A. / Lucas, M. / Moncalian, G. / Cabezas, M. / Prez-Luque, R. / Gomis-Rth, 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. / Prez-Luque, R. / Gomis-Rth, F.X. / de la Cruz, F. / Coll, M.

History

Deposition	Sep 4, 2003	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 25, 2003	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Aug 16, 2023	Group: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	1qx0.cif.gz	91.7 KB	Display	PDBx/mmCIF format
PDB format	pdb1qx0.ent.gz	66.7 KB	Display	PDB format
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Others	Other downloads

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Validation report

Summary document	1qx0_validation.pdf.gz	385.2 KB	Display	wwPDB validaton report
Full document	1qx0_full_validation.pdf.gz	392.3 KB	Display
Data in XML	1qx0_validation.xml.gz	8.1 KB	Display
Data in CIF	1qx0_validation.cif.gz	12.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qx/1qx0 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/1qx0	HTTPS FTP

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Related structure data

Related structure data	1omhSC 1osbC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2cdm-2 4pcb-2 1s6m-d 1osb-2 1zm5-d 5zt6-d 3h1w-d 3bnw-d 4h0n-3 1osb-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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TATA-Binding Protein
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RecA and Rad51
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Cascade and CRISPR
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Enhanceosome
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#112 - Apr 2009
Oct and Sox Transcription Factors
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Transposase
similarity (1)
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Integrase
similarity (1)
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TAL Effectors
similarity (1)
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Telomerase
similarity (1)
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Catabolite Activator Protein
similarity (1)
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Sliding Clamps
similarity (1)
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similarity (1)
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Zinc Fingers
similarity (1)
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similarity (1)
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RNA Polymerase
similarity (1)
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Vitamin D Receptor
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#23 - Nov 2001
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similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#240 - Dec 2019
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similarity (1)
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similarity (1)
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similarity (1)
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Twenty Years of Molecules
similarity (1)

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Assembly

Deposited unit

B: DNA OLIGONUCLEOTIDE

A: trwC protein

hetero molecules

41 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	91.185, 91.185, 205.034
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

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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 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-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H₂O

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Experimental details

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal

Density Matthews: 2.99 Å³/Da / Density % sol: 58.91 %

Crystal grow

pH: 4.6 / Details: pH 4.60

Crystal grow

*PLUS

Temperature: 4 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details
1	6 mg/ml	protein	1	drop
2	25 %(w/v)	PEG2000 MME	1	reservoir
3	0.2 M	ammonium sulfate	1	reservoir
4	0.1 M	sodium acetate	1	reservoir	pH4.6

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9839
Detector	Type: MARRESEARCH / Detector: CCD / Date: Dec 17, 2002
Radiation	Monochromator: DIAMON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9839 Å / Relative weight: 1
Reflection	Resolution: 2.26→43 Å / Num. obs: 24256 / % possible obs: 99.3 % / Redundancy: 4.4 % / R_merge(I) obs: 0.115 / Net I/σ(I): 3.6
Reflection shell	Highest resolution: 2.26 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.471 / Mean I/σ(I) obs: 1.4 / % possible all: 96.7

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
CNS		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 1OMH

1omh

Resolution: 2.26→43 Å / Cor.coef. F_o:F_c: 0.922 / Cor.coef. F_o:F_c free: 0.888 / SU B: 6.974 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.302 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor

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