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- PDB-2gie: HincII bound to cognate DNA GTTAAC -

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Basic information

Entry
Database: PDB / ID: 2gie
TitleHincII bound to cognate DNA GTTAAC
Components
  • 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*G)-3'
  • Type II restriction enzyme HincII
KeywordsHYDROLASE/DNA / protein DNA complex / indirect readout / DNA intercalation / 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: 2.6 Å
AuthorsHorton, N.C. / Joshi, H.K. / Etzkorn, C. / Chatwell, L. / Bitinaite, J.
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 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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*G)-3'
F: 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*G)-3'
G: 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*G)-3'
H: 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*G)-3'
A: Type II restriction enzyme HincII
B: Type II restriction enzyme HincII
C: Type II restriction enzyme HincII
D: Type II restriction enzyme HincII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,2749
Polymers135,2518
Non-polymers231
Water9,152508
1
E: 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*G)-3'
F: 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*G)-3'
A: Type II restriction enzyme HincII
B: Type II restriction enzyme HincII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6485
Polymers67,6254
Non-polymers231
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*G)-3'
H: 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*G)-3'
C: Type II restriction enzyme HincII
D: Type II restriction enzyme HincII


Theoretical massNumber of molelcules
Total (without water)67,6254
Polymers67,6254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.243, 175.472, 253.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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


Mass: 3992.598 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
Type II restriction enzyme HincII / E.C.3.1.21.4 / Endonuclease HincII / R.HincII


Mass: 29820.066 Da / Num. of mol.: 4
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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 4K, 0.15 M NaCl, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 4K11
2NaClSodium chloride11
3citrateCitric acid11
4H2O11
5PEG 4K12
6NaClSodium chloride12
7citrateCitric acid12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2003
RadiationMonochromator: 180 frames, 1 degree oscillation each, 100 sec
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 46277 / % possible obs: 97.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 62.5 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 11
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 2 / % possible all: 95.7

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Processing

Software
NameClassification
ADSCdata collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TX3

1tx3


Resolution: 2.6→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.306 2269 Random 5%
Rwork0.238 --
obs0.226 42973 -
all-45242 -
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8231 1060 1 508 9800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_bond_d0.006

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