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- PDB-3dvo: SgrAI with cognate DNA and calcium bound -

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Basic information

Entry
Database: PDB / ID: 3dvo
TitleSgrAI with cognate DNA and calcium bound
Components
  • DNA (5'-D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DTP*DC)-3')
  • SgraIR restriction enzyme
KeywordsHYDROLASE/DNA / restriction enzyme-DNA complex / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 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 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2020Group: Data collection / Database references / Source and taxonomy
Category: pdbx_entity_src_syn / reflns / struct_ref_seq_dif
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
E: DNA (5'-D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DTP*DC)-3')
F: DNA (5'-D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DTP*DC)-3')
G: DNA (5'-D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DTP*DC)-3')
H: DNA (5'-D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DTP*DC)-3')
A: SgraIR restriction enzyme
B: SgraIR restriction enzyme
C: SgraIR restriction enzyme
D: SgraIR restriction enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,15916
Polymers173,8388
Non-polymers3218
Water13,980776
1
E: DNA (5'-D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DTP*DC)-3')
F: DNA (5'-D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DTP*DC)-3')
A: SgraIR restriction enzyme
B: SgraIR restriction enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0798
Polymers86,9194
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10620 Å2
ΔGint-114 kcal/mol
Surface area29700 Å2
MethodPISA
2
G: DNA (5'-D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DTP*DC)-3')
H: DNA (5'-D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DTP*DC)-3')
C: SgraIR restriction enzyme
D: SgraIR restriction enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0798
Polymers86,9194
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10470 Å2
ΔGint-110 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.136, 119.248, 123.799
Angle α, β, γ (deg.)90.00, 95.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 5517.567 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: includes the SgrAI recognition sequence / Source: (synth.) synthetic construct (others)
#2: Protein
SgraIR restriction enzyme


Mass: 37941.906 Da / Num. of mol.: 4 / 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.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 776 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: PEG4000, buffer, 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: BL9-2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.89 Å / Num. obs: 126080 / % possible obs: 92.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3dpg

3dpg


Resolution: 1.892→41.068 Å / SU ML: 0.36 / Phase error: 28.53 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2732 2166 1.72 %
Rwork0.2202 --
obs0.2211 126065 92.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.445 Å2 / ksol: 0.401 e/Å3
Refinement stepCycle: LAST / Resolution: 1.892→41.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10556 1464 8 776 12804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812428
X-RAY DIFFRACTIONf_angle_d1.25517180
X-RAY DIFFRACTIONf_dihedral_angle_d19.9054660
X-RAY DIFFRACTIONf_chiral_restr0.0761894
X-RAY DIFFRACTIONf_plane_restr0.0062018

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