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- PDB-2fok: STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI -

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Basic information

Entry
Database: PDB / ID: 2fok
TitleSTRUCTURE OF RESTRICTION ENDONUCLEASE FOKI
ComponentsFOKI RESTRICTION ENDONUCLEASE
KeywordsNUCLEIC ACID RECOGNITION / DNA-BINDING PROTEIN / TYPE IIS RESTRICTION ENDONUCLEASE / DEOXYRIBONUCLEASE / DNA HYDROLYSIS / DNA CLEAVAGE / METALLOENZYME / METAL ION CATALYSIS
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding
Similarity search - Function
FokI Restriction Endonuclease; Chain A, domain 1 / Foki Restriction Endonuclease, Chain A, domain 1 / FokI, recognition domain, subdomain 2 / FokI, recognition domain, subdomain 1 / FokI, cleavage domain / FokI, D3 domain / FokI, recognition domain, subdomain 1 and 2 / FokI, recognition domain, subdomain 2 / FokI, recognition domain, subdomain 1 / FokI, cleavage domain ...FokI Restriction Endonuclease; Chain A, domain 1 / Foki Restriction Endonuclease, Chain A, domain 1 / FokI, recognition domain, subdomain 2 / FokI, recognition domain, subdomain 1 / FokI, cleavage domain / FokI, D3 domain / FokI, recognition domain, subdomain 1 and 2 / FokI, recognition domain, subdomain 2 / FokI, recognition domain, subdomain 1 / FokI, cleavage domain / FokI, D3 domain / Restriction Endonuclease - #30 / Restriction Endonuclease / Restriction endonuclease type II-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Type II restriction enzyme FokI
Similarity search - Component
Biological speciesPlanomicrobium okeanokoites (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWah, D.A. / Bitinaite, J. / Schildkraut, I. / Aggarwal, A.K.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 1998
Title: Structure of FokI has implications for DNA cleavage.
Authors: Wah, D.A. / Bitinaite, J. / Schildkraut, I. / Aggarwal, A.K.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: FokI Dimerization is Required for DNA Cleavage
Authors: Bitinaite, J. / Wah, D.A. / Aggarwal, A.K. / Schildkraut, I.
History
DepositionMar 30, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FOKI RESTRICTION ENDONUCLEASE
B: FOKI RESTRICTION ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)131,6672
Polymers131,6672
Non-polymers00
Water9,296516
1
A: FOKI RESTRICTION ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)65,8341
Polymers65,8341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FOKI RESTRICTION ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)65,8341
Polymers65,8341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.010, 137.170, 188.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FOKI RESTRICTION ENDONUCLEASE / R.FOKI


Mass: 65833.625 Da / Num. of mol.: 2 / Fragment: FULL-LENGTH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planomicrobium okeanokoites (bacteria) / Strain: IFO12536 / Gene: FOKI / Production host: Escherichia coli (E. coli)
References: UniProt: P14870, type II site-specific deoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.7 Å3/Da / Density % sol: 53.69 %
Description: CRYSTALS WERE FLASH FROZEN IN NITROGEN STREAM. DATA WAS COLLECTED BY OSCILLATION.
Crystal growpH: 6.5
Details: PROTEIN CRYSTALLIZED IN 22% PEG 8000, 0.4 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE, PH 6.5.
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.12 mMprotein1drop
211 %PEG80001drop
30.2 Mammonium sulfate1drop
450 mMsodium cacodylate1droppH6.5
50.2 M1dropKCl
610 mMpotassium phosphate1drop
70.5 mMdithiothreitol1drop
80.5 mMEDTA1drop
90.5 mMEGTA1drop
105 %glycerol1drop
1122 %PEG80001reservoir
120.4 Mammonium sulfate1reservoir
130.1 Msodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 20, 1997 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 61150 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 21.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.364 / % possible all: 81.9

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FOK

1fok


Resolution: 2.3→6 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: RESOLUTION-DEPENDENT WEIGHTING.
RfactorNum. reflection% reflectionSelection details
Rfree0.306 1732 3 %RANDOM
Rwork0.211 ---
obs0.211 57475 96.5 %-
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---0.3 Å20 Å2
3----0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8911 0 0 516 9427
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.63
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.121.5
X-RAY DIFFRACTIONx_mcangle_it2.962
X-RAY DIFFRACTIONx_scbond_it3.542
X-RAY DIFFRACTIONx_scangle_it4.612.5
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.323 200 3.1 %
Rwork0.214 6270 -
obs--87.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
X-RAY DIFFRACTION3TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / % reflection Rfree: 3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.63
LS refinement shell
*PLUS
Rfactor obs: 0.214

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