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- PDB-1dmu: Crystal structure of the restriction endonuclease BglI (e.c.3.1.2... -

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Basic information

Entry
Database: PDB / ID: 1dmu
TitleCrystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence
Components
  • BGLI RESTRICTION ENDONUCLEASE
  • DNA (5'-D(*AP*TP*CP*GP*CP*CP*TP*AP*AP*TP*AP*GP*GP*CP*GP*AP*T)-3')
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / ACTIVE SITE CALCIUM IONS / ALPHA/BETA STRUCTURE / A:A MISMATCH / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / metal ion binding
Similarity search - Function
Restriction endonuclease BglI / Restriction endonuclease, type II, BglI / Restriction endonuclease, type II, BglI superfamily / Restriction endonuclease BglI / ECO RV Endonuclease; Chain A / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / DNA / DNA (> 10) / Type-2 restriction enzyme BglI
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsNewman, M. / Lunnen, K. / Wilson, G. / Greci, J. / Schildkraut, I. / Phillips, S.E.V.
Citation
Journal: EMBO J. / Year: 1998
Title: Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.
Authors: Newman, M. / Lunnen, K. / Wilson, G. / Greci, J. / Schildkraut, I. / Phillips, S.E.
#1: Journal: Patent / Year: 1994
Title: Method for producing the BglI restriction endonuclease and methylase
Authors: Lunnen, K.D. / Wilson, G.G.
History
DepositionDec 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_abbrev / _citation.pdbx_database_id_patent ..._citation.journal_abbrev / _citation.pdbx_database_id_patent / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_leaving_atom_flag / _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_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

Downloads & links

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Assembly

Deposited unit
F: DNA (5'-D(*AP*TP*CP*GP*CP*CP*TP*AP*AP*TP*AP*GP*GP*CP*GP*AP*T)-3')
A: BGLI RESTRICTION ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5017
Polymers39,2622
Non-polymers2385
Water4,594255
1
F: DNA (5'-D(*AP*TP*CP*GP*CP*CP*TP*AP*AP*TP*AP*GP*GP*CP*GP*AP*T)-3')
A: BGLI RESTRICTION ENDONUCLEASE
hetero molecules

F: DNA (5'-D(*AP*TP*CP*GP*CP*CP*TP*AP*AP*TP*AP*GP*GP*CP*GP*AP*T)-3')
A: BGLI RESTRICTION ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,00114
Polymers78,5244
Non-polymers47710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)78.480, 81.600, 117.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: DNA chain DNA (5'-D(*AP*TP*CP*GP*CP*CP*TP*AP*AP*TP*AP*GP*GP*CP*GP*AP*T)-3')


Mass: 5211.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CONTAINS DNA RECOGNITION SEQUENCE OF BGLI
#2: Protein BGLI RESTRICTION ENDONUCLEASE / E.C.3.1.21.4


Mass: 34050.793 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: O68557, type II site-specific deoxyribonuclease
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 7-12% PEG 4000, 75-150MM LI2SO4, 100MM TRIS-HCL, 1:2 PROTEIN:DNA MOLAR RATIO, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1LI2SO411
2TRIS-HCLTris11
3PEG 400011
4PEG 400012
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mM1dropNaCl
41 mMEDTA1drop
57-12 %PEG40001reservoir
675-150 mM1reservoirLi2SO4
7100 mMTris-HCl1reservoir
3Tris-HCl1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.919
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 11, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 17679 / Num. obs: 17679 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 23.3
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 0.8 % / Rmerge(I) obs: 0.078 / % possible all: 57.1
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 57.1 %

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: ENGH & HUBER FOR PROTEIN AND PARKINSON ET AL. FOR DNA
Details: TO IMPOSE DOUBLE STRANDED BASE-PAIRING RESTRAINTS ON DNA, TWO OLIGONUCLEOTIDE STRANDS WERE INCLUDED IN THE ASYMMETRIC UNIT (RELATED BY CRYSTALLOGRAPHIC TWO- FOLD). THESE WERE GIVEN 0.5 ...Details: TO IMPOSE DOUBLE STRANDED BASE-PAIRING RESTRAINTS ON DNA, TWO OLIGONUCLEOTIDE STRANDS WERE INCLUDED IN THE ASYMMETRIC UNIT (RELATED BY CRYSTALLOGRAPHIC TWO- FOLD). THESE WERE GIVEN 0.5 OCCUPANCY AND WERE REFINED WITH FORCE CONSTANTS FOR VAN DER WAALS AND ELECTROSTATIC INTERACTIONS BETWEEN SYMMETRY RELATED MOLECULES SET TO ZERO. B-DNA SUGAR PUCKER RESTRAINTS WERE IMPOSED ONLY AT THE BEGINNING OF REFINEMENT. THE FOLLOWING SIDE-CHAINS CANNOT BE POSITIONED IN THE ELECTRON DENSITY MAP: GLU7, GLN15, GLU47, GLU102, GLU172, ARG186, THR224, LYS225 AND LYS259
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1704 10 %RANDOM
Rwork0.177 ---
all0.185 17482 --
obs0.183 17359 89.2 %-
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 346 8 255 2969
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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