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- PDB-1dc1: RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF T... -

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Basic information

Entry
Database: PDB / ID: 1dc1
TitleRESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD
Components
  • BSOBI RESTRICTION ENDONUCLEASE
  • DNA (5'-D(*T*AP*TP*AP*CP*TP*CP*GP*AP*GP*TP*AP*T)-3')
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / RESTRICTION ENDONUCLEASE / THERMOPHILIC ENZYME / DEGENERATE DNA RECOGNITION / 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 / metal ion binding
Similarity search - Function
Restriction endonuclease BsobI, helical domain / Restriction endonuclease, type II, AvaI/BsoBI / Restriction endonuclease, type II, AvaI/BsoBI, helical domain / Restriction endonuclease BsobI / Restriction Endonuclease - #10 / Restriction Endonuclease / Restriction endonuclease type II-like / Recoverin; domain 1 / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Restriction endonuclease BsobI, helical domain / Restriction endonuclease, type II, AvaI/BsoBI / Restriction endonuclease, type II, AvaI/BsoBI, helical domain / Restriction endonuclease BsobI / Restriction Endonuclease - #10 / Restriction Endonuclease / Restriction endonuclease type II-like / Recoverin; domain 1 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / DNA / DNA (> 10) / Type-2 restriction enzyme BsoBI
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.7 Å
Authorsvan der Woerd, M.J. / Pelletier, J.J. / Xu, S.-Y. / Friedman, A.M.
Citation
Journal: Structure / Year: 2001
Title: Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.
Authors: van der Woerd, M.J. / Pelletier, J.J. / Xu, S. / Friedman, A.M.
#1: Journal: Mol.Gen.Genet. / Year: 1996
Title: Cloning and sequence comparison of AvaI and BsoBI restriction modification systems
Authors: Ruan, H. / Lunnen, K.D. / Scott, M.E. / Moran, L.S. / Slatko, B.E. / Pelletier, J.J. / Hess, E.J. / Benner II, J. / Wilson, G.G.
History
DepositionNov 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
W: DNA (5'-D(*T*AP*TP*AP*CP*TP*CP*GP*AP*GP*TP*AP*T)-3')
C: DNA (5'-D(*T*AP*TP*AP*CP*TP*CP*GP*AP*GP*TP*AP*T)-3')
A: BSOBI RESTRICTION ENDONUCLEASE
B: BSOBI RESTRICTION ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,29814
Polymers81,4174
Non-polymers88110
Water8,539474
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.294, 87.823, 99.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 3965.609 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: DNA SEQUENCE DESIGNED FOR CRYSTALLIZATION BASED ON THE CENTRAL RECOGNITION SEQUENCE OF BACILLUS STEAROTHERMOPHILUS
#2: Protein BSOBI RESTRICTION ENDONUCLEASE / E.C.3.1.21.4 / TYPE II RESTRICTION ENZYME / TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE


Mass: 36742.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: P70985, type II site-specific deoxyribonuclease
#3: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.11 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: EQUILIBRATION AGAINST RESERVOIR OF 20% (V/V) DIOXANE, 2% (V/V) ETHYLENE GLYCOL AND 5 MM DTT. DROPS WERE FORMED BY MIXING 2.5 UL PROTEIN-DNA COMPLEX (10 MG/ML PROTEIN; 1.1 FOLD MOLAR EXCESS ...Details: EQUILIBRATION AGAINST RESERVOIR OF 20% (V/V) DIOXANE, 2% (V/V) ETHYLENE GLYCOL AND 5 MM DTT. DROPS WERE FORMED BY MIXING 2.5 UL PROTEIN-DNA COMPLEX (10 MG/ML PROTEIN; 1.1 FOLD MOLAR EXCESS DNA) IN BUFFER (20 MM TRIS-HCL PH 7.6, 300 MM NACL, 0.1 MM EDTA, 1 MM DTT, 0.02% NA AZIDE) WITH 2.5 UL DISTILLED WATER, 2.5 UL RESERVOIR SOLUTION AND 1.5 UL 350 MM N-HEPTYL-B-D-GLUCOSIDE, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1TRIS HCL11
2NACLSodium chloride11
3EDTAEthylenediaminetetraacetic acid11
4N-HEPTYL-B-D-GLUCOSIDE11
5NAN311
6DTT11
7DIOXANE1,4-Dioxane11
8ETHYLENE GLYCOL11
9DTT12
10DIOXANE1,4-Dioxane12
11ETHYLENE GLYCOL12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19.3 mg/mlprotein1drop
220 %(v/v)p-dioxane1reservoir
32 %(v/v)ethylene glycol1reservoir
45 mMdithiothreitol1reservoir
5350 mMn-heptyl-beta-D-glucoside1drop
61
71
81
91
101
111

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 77509 / Num. obs: 77509 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 24.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.1 / % possible all: 95.4
Reflection
*PLUS

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: ENGH & HUBER AND PARKINSON ET AL.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3845 5.1 %RANDOM
Rwork0.19 ---
obs0.19 75657 99.4 %-
all-77509 --
Displacement parametersBiso mean: 23.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.096 Å20 Å2
3---4.462 Å2
Refine analyzeLuzzati coordinate error obs: 0.197 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4997 490 60 474 6021
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.6
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
Refine LS restraints NCSRms dev position: 0.0991 Å / Weight Biso : 300 / Weight position: 2
LS refinement shellResolution: 1.7→1.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.45 458 5 %
Rwork0.402 8424 -
obs--96.9 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5.1 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.6
LS refinement shell
*PLUS
Rfactor Rfree: 0.45 / % reflection Rfree: 5 % / Rfactor Rwork: 0.402

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