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- PDB-2aud: Unliganded HincII -

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Basic information

Entry
Database: PDB / ID: 2aud
TitleUnliganded HincII
ComponentsType II restriction enzyme HincII
KeywordsHYDROLASE / restriction endonuclease / DNA binding / blunt cutter
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
Type II restriction enzyme HincII
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHorton, N.C. / Little, E.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: DNA-induced conformational changes in Type II restriction endonucleases: The structure of unliganded HincII
Authors: Horton, N.C. / Little, E.J.
History
DepositionAug 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type II restriction enzyme HincII


Theoretical massNumber of molelcules
Total (without water)29,8351
Polymers29,8351
Non-polymers00
Water8,071448
1
A: Type II restriction enzyme HincII

A: Type II restriction enzyme HincII


Theoretical massNumber of molelcules
Total (without water)59,6702
Polymers59,6702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area2630 Å2
ΔGint-30 kcal/mol
Surface area23390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.74, 59.74, 164.44
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-315-

HOH

Detailsbiological unit is a dimer. Assymetric unit contains a monomer. The dimer is created by a crystallographic twofold.

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Components

#1: Protein Type II restriction enzyme HincII / Endonuclease HincII / R.HincII


Mass: 29835.082 Da / Num. of mol.: 1 / Fragment: HincII
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: hincIIR / Production host: Escherichia coli (E. coli)
References: UniProt: P17743, type II site-specific deoxyribonuclease
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4K, Tris, NaCl, MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 18087 / Num. obs: 18087 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 52.1 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 36.6
Reflection shellResolution: 2.1→2.141007 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 5 / Num. unique all: 1013 / Rsym value: 0.297 / % possible all: 97.9

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KC6, HincII bound to DNA monomer

1kc6


Resolution: 2.1→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.327 883 5 %random
Rwork0.248 ---
all0.248 17967 --
obs0.248 17084 98.6 %-
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 0 448 2387

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