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- PDB-6ekr: Crystal structure of Type IIP restriction endonuclease Kpn2I -

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Basic information

Entry
Database: PDB / ID: 6ekr
TitleCrystal structure of Type IIP restriction endonuclease Kpn2I
ComponentsType ii site-specific deoxyribonuclease
KeywordsHYDROLASE / Restriction endonuclease / PD-(D/E)xK nuclease
Function / homologytype II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / Type ii site-specific deoxyribonuclease
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.88 Å
AuthorsTamulaitiene, G. / Manakova, E. / Grazulis, S. / Siksnys, V.
Funding supportLithuania, 2items
OrganizationGrant numberCountry
Research Council of LithuaniaMIP-41/2013Lithuania
European UnionBioStruct-X (grant agreement 283570)
CitationJournal: To Be Published
Title: Crystal structure of Type IIP restriction endonuclease PfoI with cognate DNA
Authors: Tamulaitiene, G. / Manakova, E. / Jovaisaite, V. / Grazulis, S. / Siksnys, V.
History
DepositionSep 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type ii site-specific deoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8566
Polymers36,3751
Non-polymers4805
Water46826
1
A: Type ii site-specific deoxyribonuclease
hetero molecules

A: Type ii site-specific deoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,71112
Polymers72,7502
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555x,-y,-z+1/21
Buried area3460 Å2
ΔGint-99 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.794, 134.794, 134.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-405-

SO4

21A-405-

SO4

31A-513-

HOH

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Components

#1: Protein Type ii site-specific deoxyribonuclease


Mass: 36375.191 Da / Num. of mol.: 1 / Mutation: K185A,K187A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q93K38, type II site-specific deoxyribonuclease
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.93 Å3/Da / Density % sol: 57.97 % / Description: small cubic crystals (30-50 mkm)
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystallization buffer: 0.1M NaHepes pH7.5, 1.4M ammonium sulfate and glycerol 10%. Complex of Kpn2I with DNA was used at concentration 2-7.5mg/ml
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.98019,0.98029,0.97789
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.980191
20.980291
30.977891
ReflectionResolution: 2.88→95.31 Å / Num. obs: 9398 / % possible obs: 100 % / Redundancy: 39.8 % / Biso Wilson estimate: 62.9 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.021 / Rrim(I) all: 0.134 / Rsym value: 0.116 / Net I/σ(I): 28.3
Reflection shellResolution: 2.88→3.04 Å / Redundancy: 34.6 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 1347 / Rpim(I) all: 0.093 / Rrim(I) all: 0.555 / Rsym value: 0.537 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALACCP4 6.2: Scala version 3.3.20 : 23/06/11data scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 2.88→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: FREE R-VALUE / ESU R Free: 0.432 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26398 959 10.3 %RANDOM
Rwork0.20944 ---
obs0.21498 8353 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 56.086 Å2
Refinement stepCycle: 1 / Resolution: 2.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 25 26 2503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222532
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.141.9583427
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5865302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4323.525122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26215429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7961516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021917
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.21150
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21730
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5791.51510
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08122451
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.21631022
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9414.5976
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.882→2.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 65 -
Rwork0.274 612 -
obs--100 %

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