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- PDB-3dpg: SgrAI with noncognate DNA bound -

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Basic information

Entry
Database: PDB / ID: 3dpg
TitleSgrAI with noncognate DNA bound
Components
  • DNA (5'-D(*DAP*DAP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DT)-3')
  • SgraIR restriction enzyme
KeywordsHYDROLASE/DNA / RESTRICTION ENZYME-DNA COMPLEX / BASE-PAIR MISMATCH / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


identical protein binding / 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
DNA / DNA (> 10) / SgraIR restriction enzyme
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.91 Å
AuthorsDunten, P.W. / Horton, N.C. / Little, E.J.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: The structure of SgrAI bound to DNA; recognition of an 8 base pair target.
Authors: Dunten, P.W. / Little, E.J. / Gregory, M.T. / Manohar, V.M. / Dalton, M. / Hough, D. / Bitinaite, J. / Horton, N.C.
History
DepositionJul 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Category: reflns / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_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
C: DNA (5'-D(*DAP*DAP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DT)-3')
D: DNA (5'-D(*DAP*DAP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DT)-3')
A: SgraIR restriction enzyme
B: SgraIR restriction enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5498
Polymers86,3894
Non-polymers1604
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-100 kcal/mol
Surface area29480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.726, 78.621, 86.834
Angle α, β, γ (deg.)90.00, 109.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(*DAP*DAP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DT)-3')


Mass: 5252.410 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein SgraIR restriction enzyme


Mass: 37941.906 Da / Num. of mol.: 2 / Mutation: N63D
Source method: isolated from a genetically manipulated source
Details: coexpressed with MspI methyltransferase from pBAKMspIM
Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: sgraIR / Plasmid: pET21a_SgrAIR / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q9F6L0, type II site-specific deoxyribonuclease
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: PEG4000, NaCl, CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2NaClSodium chloride11
3CaCl211
4PEG400012
5NaClSodium chloride12
6CaCl212

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionHighest resolution: 1.91 Å / Num. obs: 66598 / % possible obs: 96.1 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
DMphasing
RefinementResolution: 1.91→31.257 Å / SU ML: 0.27 / Phase error: 23.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 2017 3.03 %
Rwork0.1855 --
obs0.1867 66579 96.41 %
all-69070 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.577 Å2 / ksol: 0.41 e/Å3
Refinement stepCycle: LAST / Resolution: 1.91→31.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5372 707 4 471 6554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056290
X-RAY DIFFRACTIONf_angle_d0.9588694
X-RAY DIFFRACTIONf_dihedral_angle_d18.5782365
X-RAY DIFFRACTIONf_chiral_restr0.063951
X-RAY DIFFRACTIONf_plane_restr0.0041029

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