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- PDB-1ijw: Testing the Water-Mediated Hin Recombinase DNA Recognition by Sys... -

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Basic information

Entry
Database: PDB / ID: 1ijw
TitleTesting the Water-Mediated Hin Recombinase DNA Recognition by Systematic Mutations.
Components
  • 5'-D(*AP*TP*(CBR)P*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3'
  • 5'-D(*TP*GP*TP*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 / BR18 / 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 / SYNCHROTRON / MIRAS / Resolution: 2.4 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
DepositionApr 30, 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 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 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*TP*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3'
B: 5'-D(*AP*TP*(CBR)P*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3'
C: DNA-INVERTASE HIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9275
Polymers14,6833
Non-polymers2442
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.749, 81.136, 44.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain 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: obtained synthetically
#2: DNA chain 5'-D(*AP*TP*(CBR)P*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3'


Mass: 4310.702 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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.66 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Hanging drop vapor diffusion at 4C, with initial concentration in drop of 0.13 mM DNA, 0.33 mM Hin, 46 mMTris (pH 8.5), 46 mM CaCl2, 63 mM NaCl, 11.6% v/v PEG400, and 2.03 mM Na cacodylate. ...Details: Hanging drop vapor diffusion at 4C, with initial concentration in drop of 0.13 mM DNA, 0.33 mM Hin, 46 mMTris (pH 8.5), 46 mM CaCl2, 63 mM NaCl, 11.6% v/v PEG400, and 2.03 mM Na cacodylate. Reservoir solution contains 100 mM Tris (pH 8.5), 100 mM CaCl2, 100 mM NaCl, and 25% PEG400. Concentration of PEG400 in reservoir solution was increased in 5% increments to 35%., VAPOR DIFFUSION, HANGING DROP, temperature 281K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris11
2CaCl211
3NaCl11
4PEG 40011
5sodium cacodylate11
6Tris12
7CaCl212
8NaCl12
9PEG 40012
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mM1reservoirpH8.5NaCl/CaCl2/Tris
225 %PEG4001reservoir
31
41
51
61
71
81
91

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Data collection

DiffractionMean temperature: 100 K
Details: MULTIPLE WAVELENGTH WITH ANOMALOUS SCATTERING USING THREE IODINE AND ONE BROMINE DERIVATIVES. THE IODINE DERIVATIVES REPLACE THYMINE AT POSITIONS 4, 5, AND 7+19 WITH 5-IODO URACIL. THE ...Details: MULTIPLE WAVELENGTH WITH ANOMALOUS SCATTERING USING THREE IODINE AND ONE BROMINE DERIVATIVES. THE IODINE DERIVATIVES REPLACE THYMINE AT POSITIONS 4, 5, AND 7+19 WITH 5-IODO URACIL. THE BROMINE DERIVATIVE REPLACES CYTOSINE AT POSITION 18 WITH 5-BROMO CYTOSINE.
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.917
DetectorDetector: CCD / Date: Jun 1, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 5435 / % possible obs: 85.35 % / Observed criterion σ(I): 0 / Redundancy: 26 % / Biso Wilson estimate: 47 Å2 / Rsym value: 0.079 / Net I/σ(I): 16.59
Reflection shellResolution: 2.4→2.51 Å / Redundancy: 1.91 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.27 / % possible all: 43.76
Reflection
*PLUS
% possible obs: 85.4 % / Redundancy: 26 % / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 43.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.6

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Processing

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

Resolution: 2.4→30 Å / Data cutoff high rms absF: 10000 / Isotropic thermal model: ANISOTROPIC_FIXED_ISOTROPIC / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.278 536 8.4 %RANDOM
Rwork0.223 ---
obs0.223 5435 85.4 %-
Solvent computationBsol: 50 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1-14.66 Å20 Å20 Å2
2--4.55 Å20 Å2
3----19.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms358 576 17 7 958
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0087
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_deg1.819
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.88
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.846
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.91.5
X-RAY DIFFRACTIONc_mcangle_it8.23
X-RAY DIFFRACTIONc_scbond_it9.83
X-RAY DIFFRACTIONc_scangle_it12.63.5
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.421 39 5.1 %
Rwork0.424 337 -
obs--43.8 %
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
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.279
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.88
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.846
X-RAY DIFFRACTIONc_mcbond_it5.91.5
X-RAY DIFFRACTIONc_scbond_it9.83
X-RAY DIFFRACTIONc_mcangle_it8.23
X-RAY DIFFRACTIONc_scangle_it12.63.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.421 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.424 / Rfactor obs: 0.424

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