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- PDB-2gii: Q138F HincII bound to cognate DNA GTTAAC -

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Basic information

Entry
Database: PDB / ID: 2gii
TitleQ138F HincII bound to cognate DNA GTTAAC
Components
  • 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*GP*C)-3'
  • Type II restriction enzyme HincII
KeywordsHYDROLASE/DNA / protein DNA complex / indirect readout / DNA intercalation / endonuclease / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding
Similarity search - Function
Restriction endonuclease, type II, HincII / Restriction endonuclease HincII / DNA mismatch repair MutH/Restriction endonuclease, type II / DNA mismatch repair MutH/Type II restriction endonuclease superfamily / ECO RV Endonuclease; Chain A / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Type II restriction enzyme HincII / Type II restriction enzyme HindII
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHorton, N.C. / Joshi, H.K.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Alteration of Sequence Specificity of the Type II Restriction Endonuclease HincII through an Indirect Readout Mechanism.
Authors: Joshi, H.K. / Etzkorn, C. / Chatwell, L. / Bitinaite, J. / Horton, N.C.
History
DepositionMar 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*GP*C)-3'
F: 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*GP*C)-3'
A: Type II restriction enzyme HincII
B: Type II restriction enzyme HincII


Theoretical massNumber of molelcules
Total (without water)68,2424
Polymers68,2424
Non-polymers00
Water6,864381
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.375, 90.040, 68.009
Angle α, β, γ (deg.)90.00, 103.45, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a protein dimer bound to one duplex of DNA. The asymmetric unit contains the biological assembly.

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Components

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


Mass: 4281.779 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Type II restriction enzyme HincII / E.C.3.1.21.4 / Endonuclease HincII / R.HincII


Mass: 29839.109 Da / Num. of mol.: 2 / Mutation: Q138F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: hincIIR / Plasmid: pCCR101HincII.R / Production host: Escherichia coli (E. coli) / Strain (production host): ER2393
References: UniProt: P44413, UniProt: P17743*PLUS, type II site-specific deoxyribonuclease
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 4K, 0.15 M NaCl, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 4K11
2NaCl11
3HEPES11
4H2O11
5PEG 4K12
6NaCl12
7HEPES12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 17, 2005
RadiationMonochromator: 180 degrees, 1 degree per frame, 30 sec / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. all: 32583 / Num. obs: 32583 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 24.8

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Processing

Software
NameClassification
Blu-Icedata collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 748 2.8 %RANDOM
Rwork0.235 ---
obs0.235 26311 100 %-
all-26311 --
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3747 567 0 381 4695
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
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_deg2.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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