[English] 日本語
Yorodumi
- PDB-1osb: Conjugative Relaxase TrwC in complex with OriT Dna. Metal-free st... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
Conjugative relaxase, N-terminal / TrwC relaxase / TrwC relaxase / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / TrwC
Similarity search - Component
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 -

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more