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- PDB-1gm5: Structure of RecG bound to three-way DNA junction -

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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


chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / DNA 3'-5' helicase / DNA helicase activity / isomerase activity / DNA recombination / forked DNA-dependent helicase activity ...chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / DNA 3'-5' helicase / DNA helicase activity / isomerase activity / DNA recombination / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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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

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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

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