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- PDB-1jj8: Testing the Water-Mediated HIN Recombinase DNA Recognition by Sys... -

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Basic information

Entry
Database: PDB / ID: 1jj8
TitleTesting the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations
Components
  • 5'-D(*AP*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3'
  • 5'-D(*TP*GP*(5IT)P*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3'
  • DNA-INVERTASE HIN
KeywordsDNA BINDING PROTEIN/DNA / WATER-MEDIATED RECOGNITION / PROTEIN-DNA COMPLEX / HIN RECOMBINASE / I4 FORM 2 / 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 / SIRAS / Resolution: 2.75 Å
AuthorsChiu, T.K. / Sohn, C. / Johnson, R.C. / Dickerson, R.E.
Citation
Journal: EMBO J. / Year: 2002
Title: Testing water-mediated DNA recognition by the Hin recombinase.
Authors: Chiu, T.K. / Sohn, C. / Dickerson, R.E. / Johnson, R.C.
#1: Journal: Thesis / Year: 2001
Title: How Hin Recombinase, FIS and Cations Bind DNA. Chapter 4. Water-Mediated Sequence-Specific Recognition by Hin Recombinase.
Authors: Chiu, T.K.
#2: 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.
History
DepositionJul 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 4, 2015Group: Database references / Other
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*TP*GP*(5IT)P*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3'
B: 5'-D(*AP*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3'
C: DNA-INVERTASE HIN


Theoretical massNumber of molelcules
Total (without water)14,7163
Polymers14,7163
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.328, 68.693, 62.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-212-

HOH

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Components

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


Mass: 4436.707 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3'


Mass: 4231.806 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA-INVERTASE HIN / Hin Recombinase


Mass: 6047.051 Da / Num. of mol.: 1 / Fragment: RESIDUES 139 TO 190 / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE / References: UniProt: P03013
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.423 Å3/Da / Density % sol: 47.27 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: 0.08 MM DNA, 0.04 MM HIN, 25 MM NA ACETATE (PH 4.6), 25 MM MGCL2, 8 MM NACL, 6.3% V/V PEG400, AND 1.25 MM NA CACODYLATE. RESERVOIR SOLUTION CONTAINS 100 MM NA ACETATE (PH 4.6), 100 MM MGCL2, ...Details: 0.08 MM DNA, 0.04 MM HIN, 25 MM NA ACETATE (PH 4.6), 25 MM MGCL2, 8 MM NACL, 6.3% V/V PEG400, AND 1.25 MM NA CACODYLATE. RESERVOIR SOLUTION CONTAINS 100 MM NA ACETATE (PH 4.6), 100 MM MGCL2, AND 25% PEG400. CONCENTRATION OF PEG400 IN RESERVOIR SOLUTION WAS INCREASED IN 5% INCREMENTS TO 35%. CONDITIONS FOR NATIVE ARE THE SAME EXCEPT THE CONCENTRATION OF MGCL2 IS 5 TIMES SMALLER., pH 4.60, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1DNA11
2HIN11
3sodium acetate11
4MgCl211
5NaCl11
6PEG 40011
7sodium cacodylate11
8sodium acetate12
9MgCl212
10PEG 40012
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 4.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120-100 mM1reservoirMgCl2
2100 mM1reservoirNaOAcpH4.6
325 %PEG4001reservoir
41
51
61
71
81
91
101

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.543
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.543 Å / Relative weight: 1
ReflectionResolution: 2.75→25 Å / Num. obs: 3765 / % possible obs: 96.49 % / Observed criterion σ(I): 1 / Redundancy: 15 % / Biso Wilson estimate: 44 Å2 / Rsym value: 0.081 / Net I/σ(I): 19.6
Reflection shellResolution: 2.75→2.87 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.267 / % possible all: 91.64
Reflection
*PLUS
% possible obs: 96.5 % / Redundancy: 15 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 91.6 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 4.9

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS
Starting model: SIRAS PHASES

Resolution: 2.75→25 Å / Data cutoff high rms absF: 10000 / Isotropic thermal model: ANISOTROPIC_FIXED_ISOTROPIC / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.2771 369 9.46 %RANDOM
Rwork0.2134 ---
obs0.2134 3765 96.49 %-
Solvent computationBsol: 18.88 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 45 Å2
Baniso -1Baniso -2Baniso -3
1-9.45 Å20 Å20 Å2
2---5.107 Å20 Å2
3----4.343 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms375 552 0 12 939
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.41
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.45
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_scangle_it3.632.05
LS refinement shellResolution: 2.75→2.87 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.5136 45 9.39 %
Rwork0.3529 394 -
obs--91.64 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.41
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.45
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scangle_it3.632.05
LS refinement shell
*PLUS
Rfactor obs: 0.353

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