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- PDB-1cfr: CRYSTAL STRUCTURE OF CITROBACTER FREUNDII RESTRICTION ENDONUCLEAS... -

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Basic information

Entry
Database: PDB / ID: 1cfr
TitleCRYSTAL STRUCTURE OF CITROBACTER FREUNDII RESTRICTION ENDONUCLEASE CFR10I AT 2.15 ANGSTROMS RESOLUTION.
ComponentsRESTRICTION ENDONUCLEASE
KeywordsRESTRICTION ENDONUCLEASE / RESTRICTION ENZYME
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / metal ion binding
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
Type II restriction enzyme Cfr10I
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.15 Å
AuthorsBozic, D. / Grazulis, S. / Siksnys, V. / Huber, R.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution.
Authors: Bozic, D. / Grazulis, S. / Siksnys, V. / Huber, R.
History
DepositionFeb 2, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RESTRICTION ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)32,0511
Polymers32,0511
Non-polymers00
Water1,76598
1
A: RESTRICTION ENDONUCLEASE

A: RESTRICTION ENDONUCLEASE

A: RESTRICTION ENDONUCLEASE

A: RESTRICTION ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)128,2064
Polymers128,2064
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area9930 Å2
ΔGint-83 kcal/mol
Surface area46240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.500, 81.300, 119.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein RESTRICTION ENDONUCLEASE / CFR10I


Mass: 32051.387 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 283
Source method: isolated from a genetically manipulated source
Details: CHARACTERIZATION OF CFR10I RESTRICTION ENDONUCLEASE, JANULAITIS ET AL. (1983)
Source: (gene. exp.) Citrobacter freundii (bacteria) / Strain: RFL10I / Plasmid: PBR327 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1
References: UniProt: P56200, type II site-specific deoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
220 mMTris-HCl1drop
3200 mM1dropNaCl
41 Mammonium acetate1drop
575 mMMES1drop
61 Mammonium acetate1reservoir
775 mMMES1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.96
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionNum. obs: 15745

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.15→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.196 --
obs0.196 15396 90.2 %
Displacement parametersBiso mean: 29.34 Å2
Refinement stepCycle: LAST / Resolution: 2.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 0 98 2340
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.49
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.43
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.383
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19.PROTOPH19.PEP
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.433
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.383

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