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- PDB-1es8: Crystal structure of free BglII -

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Basic information

Entry
Database: PDB / ID: 1es8
TitleCrystal structure of free BglII
ComponentsRESTRICTION ENDONUCLEASE BGLII
KeywordsHYDROLASE / RESTRICTION ENDONUCLEASE / RESTRICTION ENZYME / uncomplexed
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / magnesium ion binding / DNA binding
Similarity search - Function
Restriction endonuclease, type II, BamHI/BglIII/BstY / Restriction Endonuclease - #20 / Restriction Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Type II restriction enzyme BglII
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsLukacs, C.M. / Aggarwal, A.K.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of free BglII reveals an unprecedented scissor-like motion for opening an endonuclease.
Authors: Lukacs, C.M. / Kucera, R. / Schildkraut, I. / Aggarwal, A.K.
History
DepositionApr 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 9, 2012Group: Source and taxonomy
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RESTRICTION ENDONUCLEASE BGLII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0922
Polymers26,0321
Non-polymers601
Water1,45981
1
A: RESTRICTION ENDONUCLEASE BGLII
hetero molecules

A: RESTRICTION ENDONUCLEASE BGLII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1844
Polymers52,0642
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Unit cell
Length a, b, c (Å)79.150, 79.150, 66.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RESTRICTION ENDONUCLEASE BGLII


Mass: 26031.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q45488, type II site-specific deoxyribonuclease
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% isopropanol, 0.2 M sodium acetate, 0.1 M Bis-tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4
Details: drop consists of equal amounts of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
210 mMTris-HCl1drop
3100 mM1dropKCl
410 %(v/v)glycerol1drop
51 mMdithiothreitol1drop
630 %(v/v)isopropanol1reservoirprecipitant
70.2 Msodium acetate1reservoirprecipitant
8100 mMBis-tris1reservoirprecipitant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9793, 0.9789, 0.9689
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Mar 1, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97891
30.96891
ReflectionResolution: 2.3→40 Å / Num. all: 10979 / Num. obs: 10979 / % possible obs: 99.4 % / Observed criterion σ(I): -2 / Redundancy: 3.1 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.152 / Num. unique all: 1083 / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 33794 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.138

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 555 5 %Random
Rwork0.214 ---
all-10963 --
obs-10963 99.6 %-
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 4 81 1677
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.27
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Num. reflection all: 10418
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.1 Å2

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