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- PDB-2c1l: Structure of the BfiI restriction endonuclease -

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Basic information

Entry
Database: PDB / ID: 2c1l
TitleStructure of the BfiI restriction endonuclease
ComponentsRESTRICTION ENDONUCLEASERestriction enzyme
KeywordsHYDROLASE / BFII / RESTRICTION ENDONUCLEASE / DOMAIN FUSION
Function / homology
Function and homology information


endonuclease activity
Similarity search - Function
At1g16640 B3 domain - #30 / Restriction endonuclease BfiI C-terminal domain / Metal-independent restriction enzyme BfiI, DNA binding domain / Metal-independent restriction enzyme BfiI DNA binding domain / At1g16640 B3 domain / Phospholipase D-like domain / PLD-like domain / Endonuclease Chain A / Endonuclease; Chain A / Beta Barrel ...At1g16640 B3 domain - #30 / Restriction endonuclease BfiI C-terminal domain / Metal-independent restriction enzyme BfiI, DNA binding domain / Metal-independent restriction enzyme BfiI DNA binding domain / At1g16640 B3 domain / Phospholipase D-like domain / PLD-like domain / Endonuclease Chain A / Endonuclease; Chain A / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / S,R MESO-TARTARIC ACID / D(-)-TARTARIC ACID / L(+)-TARTARIC ACID / Restriction endonuclease
Similarity search - Component
Biological speciesBACILLUS FIRMUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å
AuthorsGrazulis, S. / Manakova, E. / Roessle, M. / Bochtler, M. / Tamulaitiene, G. / Huber, R. / Siksnys, V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure of the Metal-Independent Restriction Enzyme Bfii Reveals Fusion of a Specific DNA-Binding Domain with a Nonspecific Nuclease.
Authors: Grazulis, S. / Manakova, E. / Roessle, M. / Bochtler, M. / Tamulaitiene, G. / Huber, R. / Siksnys, V.
History
DepositionSep 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RESTRICTION ENDONUCLEASE
B: RESTRICTION ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,83716
Polymers80,0832
Non-polymers1,75314
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)138.925, 138.925, 94.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RESTRICTION ENDONUCLEASE / Restriction enzyme / BFII RESTRICTION ENDONUCLEASE


Mass: 40041.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS FIRMUS (bacteria) / Strain: S8120 / Plasmid: PET21B-BFIIR6, 5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566
References: UniProt: Q9F4C9, type II site-specific deoxyribonuclease

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Non-polymers , 8 types, 494 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#7: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.51 Å3/Da / Density % sol: 50.66 %
Crystal growpH: 6.5 / Details: MES 0.1M PH 6.5 K/NA TARTRATE 1.1M GLYCEROL 25%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9755
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 9, 2001 / Details: MIRRORS
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 1.9→28 Å / Num. obs: 70374 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
DMphasing
CNS1refinement
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→28.01 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 31299524.91 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: RESIDUAL
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED. BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.217 7018 10 %RANDOM
Rwork0.188 ---
obs0.188 70375 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.1296 Å2 / ksol: 0.382458 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5644 0 114 480 6238
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 1138 9.7 %
Rwork0.228 10577 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3BCT.PARBCT.TOP
X-RAY DIFFRACTION4GOL.PARGOL.TOP
X-RAY DIFFRACTION5MES.PARMES.TOP
X-RAY DIFFRACTION6SRT.PARSRT.TOP
X-RAY DIFFRACTION7SST.PARSST.TOP
X-RAY DIFFRACTION8TLA.PARTLA.TOP
X-RAY DIFFRACTION9TRS.PARTRS.TOP

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