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- PDB-1fok: STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1fok
TitleSTRUCTURE OF RESTRICTION ENDONUCLEASE FOKI BOUND TO DNA
Components
  • DNA (5'-D(*AP*TP*GP*AP*CP*TP*AP*GP*CP*GP*TP*TP*AP*TP*CP*AP*T P*CP*CP*G)-3')
  • DNA (5'-D(*TP*CP*GP*GP*AP*TP*GP*AP*TP*AP*AP*CP*GP*CP*TP*AP*G P*TP*CP*A)-3')
  • PROTEIN (FOKI RESTRICTION ENDONUCLEASE)
KeywordsHYDROLASE/DNA / COMPLEX (ENDONUCLEASE-DNA) / TYPE IIS / RESTRICTION ENDONUCLEASE / DEOXYRIBONUCLEASE / DNA HYDROLYSIS / DNA CLEAVAGE / 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
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
DNA / DNA (> 10) / Type II restriction enzyme FokI
Similarity search - Component
Biological speciesPlanomicrobium okeanokoites (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å
AuthorsAggarwal, D.A. / Wah, J.A. / Hirsch, L.F. / Dorner, I. / Schildkraut, A.K.
Citation
Journal: Nature / Year: 1997
Title: Structure of the multimodular endonuclease FokI bound to DNA.
Authors: Wah, D.A. / Hirsch, J.A. / Dorner, L.F. / Schildkraut, I. / Aggarwal, A.K.
#1: Journal: FEBS Lett. / Year: 1997
Title: Crystallization and Preliminary X-Ray Analysis of Restriction Endonuclease Foki Bound to DNA
Authors: Hirsch, J.A. / Wah, D.A. / Dorner, L.F. / Schildkraut, I. / Aggarwal, A.K.
History
DepositionApr 18, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 30, 2021Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*TP*CP*GP*GP*AP*TP*GP*AP*TP*AP*AP*CP*GP*CP*TP*AP*G P*TP*CP*A)-3')
C: DNA (5'-D(*AP*TP*GP*AP*CP*TP*AP*GP*CP*GP*TP*TP*AP*TP*CP*AP*T P*CP*CP*G)-3')
A: PROTEIN (FOKI RESTRICTION ENDONUCLEASE)


Theoretical massNumber of molelcules
Total (without water)77,7863
Polymers77,7863
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.590, 119.340, 71.520
Angle α, β, γ (deg.)90.00, 101.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(*TP*CP*GP*GP*AP*TP*GP*AP*TP*AP*AP*CP*GP*CP*TP*AP*G P*TP*CP*A)-3') / R.FOKI


Mass: 6158.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planomicrobium okeanokoites (bacteria) / Strain: IFO12536 / Gene: FOKI / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(*AP*TP*GP*AP*CP*TP*AP*GP*CP*GP*TP*TP*AP*TP*CP*AP*T P*CP*CP*G)-3')


Mass: 6108.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Protein PROTEIN (FOKI RESTRICTION ENDONUCLEASE)


Mass: 65519.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planomicrobium okeanokoites (bacteria) / References: UniProt: P14870
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 7

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 62 % / Description: CRYSTALS WERE FLASH FROZEN IN NITROGEN STREAM.
Crystal growpH: 6 / Details: pH 6.00
Crystal
*PLUS
Density % sol: 62 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.15 mMprotein1drop
20.75 mMDNA1drop
31.1 Mammonium sulfate1drop
40.5 MMES1drop
50.2 M1dropKCl
610 mMpotassium phosphate1drop
70.5 mMdithiothreitol1drop
80.5 mMEDTA1drop
90.5 mMEGTA1drop
105 %glycerol1drop
112.2 Mammonium sulfate1reservoir
121.0 MMES1reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1
DetectorType: SOL GRUNER, FUJI / Detector: CCD / Date: May 3, 1994 / Details: MIRRORS
RadiationMonochromator: BENT, TRIANGULAR SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 26253 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 57.6 Å2 / Rmerge(I) obs: 0.075
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.325 / % possible all: 96.1
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 100 Å / % possible obs: 98.5 %
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 96.1 %

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Processing

Software
NameVersionClassification
PHASESphasing
CCP4model building
SOLOMONphasing
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
X-PLORphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.296 710 2.8 %RANDOM
Rwork0.214 ---
obs0.214 24931 97.9 %-
Displacement parametersBiso mean: 38.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å22.07 Å2
2---1.09 Å20 Å2
3----0.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 814 0 172 5527
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.57
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.491.5
X-RAY DIFFRACTIONx_mcangle_it5.632
X-RAY DIFFRACTIONx_scbond_it5.652
X-RAY DIFFRACTIONx_scangle_it8.362.5
LS refinement shellResolution: 2.8→2.92 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.407 90 3 %
Rwork0.354 2900 -
obs--94.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMCSDX_MOD.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM_NDBX96.DNATOP_NDBX96.DNA
X-RAY DIFFRACTION3PARAM19.SOLTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.57
LS refinement shell
*PLUS
Rfactor obs: 0.354

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