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- PDB-1hcr: HIN RECOMBINASE BOUND TO DNA: THE ORIGIN OF SPECIFICITY IN MAJOR ... -

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Basic information

Entry
Database: PDB / ID: 1hcr
TitleHIN RECOMBINASE BOUND TO DNA: THE ORIGIN OF SPECIFICITY IN MAJOR AND MINOR GROOVE INTERACTIONS
Components
  • DNA (5'-D(*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3')
  • PROTEIN (HIN RECOMBINASE)
KeywordsDNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA recombination / 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 / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-invertase hin
Similarity search - Component
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsFeng, J.-A. / Johnson, R.C. / Dickerson, R.E.
Citation
Journal: Science / Year: 1994
Title: Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions.
Authors: Feng, J.A. / Johnson, R.C. / Dickerson, R.E.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Prelimanary X-Ray Analysis of the DNA Binding Domain of the Hin Recombinase with its DNA Binding Site
Authors: Feng, J.-A. / Simon, M. / Mack, D.P. / Dervan, P.B. / Johnson, R.C. / Dickerson, R.E.
History
DepositionDec 17, 1993Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 30, 1994Provider: 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
B: DNA (5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3')
C: DNA (5'-D(*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3')
A: PROTEIN (HIN RECOMBINASE)


Theoretical massNumber of molelcules
Total (without water)14,2903
Polymers14,2903
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.920, 81.370, 44.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: LYS A 186 - LYS A 187 OMEGA =148.79 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: DNA chain DNA (5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3')


Mass: 4324.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#2: DNA chain DNA (5'-D(*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3')


Mass: 3918.599 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Protein PROTEIN (HIN RECOMBINASE)


Mass: 6047.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P03013
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 150011

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Data collection

DiffractionMean temperature: 123 K
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. all: 17839 / Num. obs: 5346 / Observed criterion σ(F): 2

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.3→8 Å / σ(F): 2
Details: THIS COORDINATE SET IS PRELIMINARY. REFINEMENT IS STILL IN PROGRESS. RESIDUES SER 183 AND SER 184 ARE POORLY DEFINED IN THE ELECTRON DENSITY MAP.
RfactorNum. reflection
Rwork0.228 -
obs0.228 5346
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms426 547 0 16 989
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.024
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_deg3.97
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

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