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- PDB-1gdt: CRYSTAL STRUCTURE OF A SITE-SPECIFIC RECOMBINASE, GAMMA-DELTA RES... -

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Basic information

Entry
Database: PDB / ID: 1gdt
TitleCRYSTAL STRUCTURE OF A SITE-SPECIFIC RECOMBINASE, GAMMA-DELTA RESOLVASE COMPLEXED WITH A 34 BP CLEAVAGE SITE
Components
  • (SITE I OF RES DNA) x 3
  • PROTEIN (GAMMA DELTA RESOLVASE)
KeywordsDNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / OVERHANGING BASE / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #10 / Resolvase, N-terminal catalytic 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #10 / Resolvase, N-terminal catalytic 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Homeodomain-like / Helix non-globular / Homeobox-like domain superfamily / Special / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transposon gamma-delta resolvase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsYang, W. / Steitz, T.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1995
Title: Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site.
Authors: Yang, W. / Steitz, T.A.
History
DepositionApr 11, 1995Processing site: NDB
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: SITE I OF RES DNA
D: SITE I OF RES DNA
E: SITE I OF RES DNA
F: SITE I OF RES DNA
A: PROTEIN (GAMMA DELTA RESOLVASE)
B: PROTEIN (GAMMA DELTA RESOLVASE)


Theoretical massNumber of molelcules
Total (without water)61,9426
Polymers61,9426
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.000, 157.000, 37.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain SITE I OF RES DNA / CROSSOVER SITE OR CLEAVAGE SITE


Mass: 6774.416 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain SITE I OF RES DNA / CROSSOVER SITE OR CLEAVAGE SITE


Mass: 3966.597 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain SITE I OF RES DNA / CROSSOVER SITE OR CLEAVAGE SITE


Mass: 6445.209 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Protein PROTEIN (GAMMA DELTA RESOLVASE) / GD RESOLVASE


Mass: 20394.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: STRAINS THAT CONTAIN F EPISOME / Gene: TNPR / Plasmid: MGH285 / Gene (production host): TNPR / Production host: Escherichia coli (E. coli) / Strain (production host): AR120 / References: UniProt: P03012
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESOLVASE GENE IS PUT UNDER THE CONTROL OF THE LAMBDA PROMOTER AND INDUCED BY NALIDIXIC ACID.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 54 %
Crystal
*PLUS
Density % sol: 54 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.36 mMresolvase monomer1drop
20.72 mMDNA modular duplex1drop
30.2 Mammonium sulfate1drop
42.5 %ethylene glycol1drop
50.5 mMEDTA1drop
610 mMTris-HCl1drop
750 mMMES1drop
815 %PEG33501drop
90.2 Mammonium sulfate1reservoir
105 %ethylene glycol1reservoir
11100 mMMES1reservoir
1230 %PRG33501reservoir

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Data collection

DiffractionMean temperature: 113 K
DetectorDate: Apr 1, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 13255 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.077
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 30 Å / % possible obs: 94.2 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.235 --
obs0.235 12130 89.5 %
Displacement parametersBiso mean: 26.69 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 1407 0 29 4284
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d33.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg33.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1

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