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- PDB-1knv: Bse634I restriction endonuclease -

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Basic information

Entry
Database: PDB / ID: 1knv
TitleBse634I restriction endonuclease
ComponentsBse634I restriction endonuclease
KeywordsHYDROLASE / Restriction endonuclease / apo-enzyme
Function / homology
Function and homology information


endonuclease activity
Similarity search - Function
Restriction Endonuclease - #10 / Restriction endonuclease, type II, Cfr10I/Bse634I / Cfr10I/Bse634I restriction endonuclease / Restriction Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Endonuclease Bse634IR
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.17 Å
AuthorsGrazulis, S. / Deibert, M. / Rimseliene, R. / Skirgaila, R. / Sasnauskas, G. / Lagunavicius, A. / Repin, V. / Urbanke, C. / Huber, R. / Siksnys, V.
CitationJournal: Nucleic Acids Res. / Year: 2002
Title: Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence.
Authors: Grazulis, S. / Deibert, M. / Rimseliene, R. / Skirgaila, R. / Sasnauskas, G. / Lagunavicius, A. / Repin, V. / Urbanke, C. / Huber, R. / Siksnys, V.
History
DepositionDec 19, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Bse634I restriction endonuclease
B: Bse634I restriction endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9939
Polymers67,6982
Non-polymers2957
Water5,224290
1
A: Bse634I restriction endonuclease
B: Bse634I restriction endonuclease
hetero molecules

A: Bse634I restriction endonuclease
B: Bse634I restriction endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,98618
Polymers135,3964
Non-polymers59114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area12210 Å2
ΔGint-184 kcal/mol
Surface area51480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)121.230, 122.280, 56.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-3145-

HOH

21A-3146-

HOH

31B-3153-

HOH

DetailsBiological assembly is a teramer (dimer of dimers); second dimer in the tetramer is generated by crystallographic two-fold axis -x+1, -y+1, z from the chains A and B

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Components

#1: Protein Bse634I restriction endonuclease


Mass: 33848.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267
References: UniProt: Q8RT53, type II site-specific deoxyribonuclease
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Na Acetate, PEG 8000, Calcium chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.10 mMprotein1droptetramer solution
220 mMTris-HCl1drop
350 mM1dropNaCl
41 mMEDTA1drop
5100 mMsodium acetate1reservoirpH5.5
612 %PEG80001reservoir
7100 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.09932 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 2, 1997 / Details: monochromator, mirrors
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09932 Å / Relative weight: 1
ReflectionResolution: 2.17→24.6 Å / Num. all: 43316 / Num. obs: 43275 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.17→2.23 Å / % possible all: 87.2
Reflection
*PLUS
Num. obs: 43316

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Processing

Software
NameVersionClassification
CCP4suitemodel building
Omodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.17→24.61 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2011306.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4314 10.1 %RANDOM
Rwork0.218 ---
all0.2213 43275 --
obs0.218 42686 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.3493 Å2 / ksol: 0.3641 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.14 Å20 Å20 Å2
2--2.32 Å20 Å2
3---1.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.17→24.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4709 0 13 290 5012
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it1.452
X-RAY DIFFRACTIONc_scangle_it2.432.5
LS refinement shellResolution: 2.17→2.3 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 673 10.5 %
Rwork0.273 5766 -
obs--86.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ACT.PARAMACT.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 43316 / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_scbond_it1.452
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scangle_it2.432.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.288 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.273

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