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- PDB-2ezv: Crystal structure of tetrameric restriction endonuclease SfiI bou... -

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Basic information

Entry
Database: PDB / ID: 2ezv
TitleCrystal structure of tetrameric restriction endonuclease SfiI bound to cognate DNA.
Components
  • 5'-D(*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*A)-3'
  • 5'-D(*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*T)-3'
  • Type II restriction enzyme SfiI
KeywordsHYDROLASE/DNA / Type IIF restriction endonuclease / protein-DNA complex / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system
Similarity search - Function
Type II restriction enzyme SfiI, DNA-recognition domain / Type II restriction enzyme SfiI, multifunctional domain / Type II restriction enzyme SfiI / Restriction endonuclease, type II SfiI, domain 2 / Restriction endonuclease, type II SfiI, domain 1 / Type II restriction enzyme SfiI / ECO RV Endonuclease; Chain A / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich ...Type II restriction enzyme SfiI, DNA-recognition domain / Type II restriction enzyme SfiI, multifunctional domain / Type II restriction enzyme SfiI / Restriction endonuclease, type II SfiI, domain 2 / Restriction endonuclease, type II SfiI, domain 1 / Type II restriction enzyme SfiI / ECO RV Endonuclease; Chain A / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Type II restriction enzyme SfiI
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAggarwal, A.K. / Vanamee, E.S. / Viadiu, H.
Citation
Journal: Embo J. / Year: 2005
Title: A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA
Authors: Vanamee, E.S. / Viadiu, H. / Kucera, R. / Dorner, L. / Picone, S. / Schildkraut, I. / Aggarwal, A.K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization of restriction endonuclease SfiI in complex with DNA.
Authors: Viadiu, H. / Vanamee, E.S. / Jacobson, E.M. / Schildkraut, I. / Aggarwal, A.K.
History
DepositionNov 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: 5'-D(*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*T)-3'
G: 5'-D(*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*A)-3'
A: Type II restriction enzyme SfiI
B: Type II restriction enzyme SfiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1386
Polymers75,0574
Non-polymers802
Water3,225179
1
F: 5'-D(*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*T)-3'
G: 5'-D(*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*A)-3'
A: Type II restriction enzyme SfiI
B: Type II restriction enzyme SfiI
hetero molecules

F: 5'-D(*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*T)-3'
G: 5'-D(*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*A)-3'
A: Type II restriction enzyme SfiI
B: Type II restriction enzyme SfiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,27512
Polymers150,1158
Non-polymers1604
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Unit cell
Length a, b, c (Å)85.600, 85.600, 202.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: x-y,-y,1/3-z

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Components

#1: DNA chain 5'-D(*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*T)-3'


Mass: 6447.185 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*A)-3'


Mass: 6438.171 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Type II restriction enzyme SfiI / Endonuclease SfiI / R.SfiI


Mass: 31086.008 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: E. coli
References: UniProt: O52512, type II site-specific deoxyribonuclease
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: pH 4.6 - 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 33075 / % possible obs: 95.9 %

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.265 1642 4.8 %
Rwork0.224 --
all-807714 -
obs-33075 95.9 %
Solvent computationBsol: 41.976 Å2
Displacement parametersBiso mean: 28.594 Å2
Baniso -1Baniso -2Baniso -3
1--1.767 Å2-3.99 Å20 Å2
2---1.767 Å20 Å2
3---3.534 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4239 609 2 179 5029
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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