[English] 日本語
Yorodumi
- PDB-1gm5: Structure of RecG bound to three-way DNA junction -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gm5
TitleStructure of RecG bound to three-way DNA junction
Components
  • DNA (5'-(*CP*AP*GP*CP*TP*CP*CP*AP*TP*GP*AP*TP* CP*AP*TP*TP*GP*GP*CP*A)-3')
  • DNA (5'-(*GP*AP*GP*CP*AP*CP*TP*GP*C)-3')
  • DNA (5'-(*GP*CP*AP*GP*TP*GP*CP*TP*CP*GP*CP*AP* TP*GP*GP*AP*GP*CP*TP*G)-3')
  • RECG
KeywordsHELICASE / REPLICATION RESTART
Function / homology
Function and homology information


DNA 3'-5' helicase / DNA helicase activity / DNA recombination / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
RecG, N-terminal domain / ATP-dependent DNA helicase RecG / RecG, N-terminal antiparallel four helix bundle / RecG, wedge domain / RecG, N-terminal domain superfamily / ATP-dependent DNA helicase RecG, domain 3, C-terminal / RecG N-terminal helical domain / RecG wedge domain / ATP-dependent DNA helicase RecG, domain 3, C-terminal / : ...RecG, N-terminal domain / ATP-dependent DNA helicase RecG / RecG, N-terminal antiparallel four helix bundle / RecG, wedge domain / RecG, N-terminal domain superfamily / ATP-dependent DNA helicase RecG, domain 3, C-terminal / RecG N-terminal helical domain / RecG wedge domain / ATP-dependent DNA helicase RecG, domain 3, C-terminal / : / Nucleic acid-binding proteins / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helicase conserved C-terminal domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / ATP-dependent DNA helicase RecG
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.24 Å
AuthorsSingleton, M.R. / Scaife, S. / Wigley, D.B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structural Analysis of DNA Replication Fork Reversal by Recg
Authors: Singleton, M.R. / Scaife, S. / Wigley, D.B.
History
DepositionSep 11, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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.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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RECG
X: DNA (5'-(*CP*AP*GP*CP*TP*CP*CP*AP*TP*GP*AP*TP* CP*AP*TP*TP*GP*GP*CP*A)-3')
Y: DNA (5'-(*GP*CP*AP*GP*TP*GP*CP*TP*CP*GP*CP*AP* TP*GP*GP*AP*GP*CP*TP*G)-3')
Z: DNA (5'-(*GP*AP*GP*CP*AP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,5366
Polymers105,0854
Non-polymers4522
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)133.704, 144.602, 84.023
Angle α, β, γ (deg.)90.00, 113.82, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein RECG


Mass: 90059.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q9WY48

-
DNA chain , 3 types, 3 molecules XYZ

#2: DNA chain DNA (5'-(*CP*AP*GP*CP*TP*CP*CP*AP*TP*GP*AP*TP* CP*AP*TP*TP*GP*GP*CP*A)-3')


Mass: 6093.955 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-(*GP*CP*AP*GP*TP*GP*CP*TP*CP*GP*CP*AP* TP*GP*GP*AP*GP*CP*TP*G)-3')


Mass: 6190.990 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain DNA (5'-(*GP*AP*GP*CP*AP*CP*TP*GP*C)-3')


Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.21 %
Crystal growpH: 5 / Details: pH 5.00
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
21 mMdithiothreitol1drop
3200 mM1dropNaCl
410 mMTris-HCl1drop
5500 mMpotassium phosphate1reservoir
65 mM1reservoirMgCl2
71 mMADP1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.25→20 Å / Num. obs: 22945 / % possible obs: 98.3 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.039
Reflection
*PLUS
Lowest resolution: 20 Å

-
Processing

SoftwareName: REFMAC / Version: 5 / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 3.24→20 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.876 / SU B: 34.392 / SU ML: 0.598 / Cross valid method: THROUGHOUT / ESU R Free: 0.604 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.328 1191 5.2 %RANDOM
Rwork0.272 ---
obs0.275 21822 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 94.26 Å2
Baniso -1Baniso -2Baniso -3
1-5.86 Å20 Å24.7 Å2
2--1.84 Å20 Å2
3----3.9 Å2
Refinement stepCycle: LAST / Resolution: 3.24→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5919 832 28 0 6779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226989
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6072.1349587
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1813725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg30.826151209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1410.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024890
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.5160.34771
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3650.5586
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.9120.3125
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5740.55
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.14933621
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it16.21165854
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it17.80463368
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it24.785103732
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: 3.24→3.32 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.404 70
Rwork0.322 1417
Software
*PLUS
Version: 5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONp_bond_d0.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.6
X-RAY DIFFRACTIONp_chiral_restr0.2
X-RAY DIFFRACTIONp_mcbond_it3
X-RAY DIFFRACTIONp_scbond_it6
X-RAY DIFFRACTIONp_mcangle_it6
X-RAY DIFFRACTIONp_scangle_it10

+
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://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