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- PDB-1gdr: MODEL FOR A DNA MEDIATED SYNAPTIC COMPLEX SUGGESTED BY CRYSTAL PA... -

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Basic information

Entry
Database: PDB / ID: 1gdr
TitleMODEL FOR A DNA MEDIATED SYNAPTIC COMPLEX SUGGESTED BY CRYSTAL PACKING OF GAMMA DELTA RESOLVASE SUBUNITS
ComponentsGAMMA DELTA-RESOLVASE
KeywordsSITE-SPECIFIC RECOMBINASE
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA binding
Similarity search - Function
Site-specific recombinases signature 2. / Resolvase, HTH domain / Helix-turn-helix domain of resolvase / Recombinase, conserved site / Site-specific recombinases active site. / : / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain ...Site-specific recombinases signature 2. / Resolvase, HTH domain / Helix-turn-helix domain of resolvase / Recombinase, conserved site / Site-specific recombinases active site. / : / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Transposon gamma-delta resolvase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsRice, P.A. / Steitz, T.A.
Citation
Journal: EMBO J. / Year: 1994
Title: Model for a DNA-mediated synaptic complex suggested by crystal packing of gamma delta resolvase subunits.
Authors: Rice, P.A. / Steitz, T.A.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1990
Title: The Crystal Structure of the Catalytic Domain of the Site Specific Recombination Enzyme Gd Resolvase at 2.7 Resolution
Authors: Sanderson, M.R. / Freemont, P.S. / Rice, P.A. / Goldman, A. / Hatfull, G.F. / Grindley, N.D.F.
#2: Journal: J.Biol.Chem. / Year: 1986
Title: Preliminary X-Ray Diffraction Studies of the Putative Catalytic Domain of Gd Resolvase from Escherichia Coli
Authors: Abdel-Meguid, S.S. / Murthy, H.M.K. / Steitz, T.A.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1984
Title: Cleavage of the Site-Specific Recombination Protein Gd Resolvase: The Smaller of Two Fragments Binds DNA Specifically
Authors: Abdel-Muguid, S.S. / Grindley, N.D.F. / Templeton, N.S. / Steitz, T.A.
#4: Journal: J.Mol.Biol. / Year: 1982
Title: Crystallization of Resolvase, a Repressor that Also Catalyzes Site-Specific DNA Recombination
Authors: Weber, P.C. / Ollis, D.L. / Bebrin, W.R. / Abdel-Meguid, S.S. / Steitz, T.A.
History
DepositionAug 31, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GAMMA DELTA-RESOLVASE


Theoretical massNumber of molelcules
Total (without water)15,5161
Polymers15,5161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.200, 60.200, 170.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsTHE MATRIX GIVEN BELOW WILL APPROXIMATELY SUPERIMPOSE MONOMER-B FROM THE C2221 CRYSTAL STRUCTURE ONTO THE THE STRUCTURE PRESENTED IN THIS ENTRY. 0.77672 0.02093 -0.62949 (X - 25.22352) + -9.96070 0.62967 -0.00232 0.77686 (X - 53.97461) + 43.29039 0.01480 -0.99978 -0.01498 (X - 47.00185) + 12.88526

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Components

#1: Protein GAMMA DELTA-RESOLVASE / Coordinate model: Cα atoms only


Mass: 15515.833 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P03012
Compound detailsTHESE CRYSTALS DO NOT DIFFRACT AS WELL AS THE C2221 CRYSTAL FORM (PDB ENTRY 2RSL) AND ARE MAINLY OF ...THESE CRYSTALS DO NOT DIFFRACT AS WELL AS THE C2221 CRYSTAL FORM (PDB ENTRY 2RSL) AND ARE MAINLY OF INTEREST IN REGARDS TO CRYSTAL PACKING. THE AUTHORS HAVE PROPOSED A MODEL OF THE SYNAPTIC COMPLEX BASED ON THE PACKING OF PROTOMERS IN THIS UNIT CELL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal grow
*PLUS
Temperature: 30 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
124 mg/mlprotein1drop
225-35 %sat1drop(NH4)2SO4
350 mMNa acetate1drop
450 mMNa acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 3.3 Å / Num. obs: 3455 / % possible obs: 85 % / Rmerge(I) obs: 0.049

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.31 / Rfactor obs: 0.31 / Highest resolution: 3.5 Å
Refinement stepCycle: LAST / Highest resolution: 3.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms105 0 0 0 105
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.55
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.5 Å / Rfactor obs: 0.31
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.55

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