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- PDB-3n78: SgrAI bound to Secondary Site DNA and Mg(II) -

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Basic information

Entry
Database: PDB / ID: 3n78
TitleSgrAI bound to Secondary Site DNA and Mg(II)
Components
  • DNA (5'-D(*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*GP*GP*GP*AP*CP*T)-3')
  • DNA (5'-D(*AP*GP*TP*CP*CP*CP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
  • SgraIR restriction enzyme
KeywordsHYDROLASE/DNA / restriction endonuclease / 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 / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsHorton, N.C. / Little, E.J. / Dunten, P.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: New clues in the allosteric activation of DNA cleavage by SgrAI: structures of SgrAI bound to cleaved primary-site DNA and uncleaved secondary-site DNA.
Authors: Little, E.J. / Dunten, P.W. / Bitinaite, J. / Horton, N.C.
History
DepositionMay 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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_ref_seq_dif / 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_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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
A: SgraIR restriction enzyme
B: SgraIR restriction enzyme
C: DNA (5'-D(*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*GP*GP*GP*AP*CP*T)-3')
D: DNA (5'-D(*AP*GP*TP*CP*CP*CP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7326
Polymers85,6834
Non-polymers492
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-82 kcal/mol
Surface area28400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.794, 133.002, 64.623
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsAUTHORS STATE THAT THE ENZYME IS DIMERIC, AND IS BOUND TO ONE DUPLEX OF DNA.

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Components

#1: Protein SgraIR restriction enzyme


Mass: 37941.906 Da / Num. of mol.: 2 / Mutation: N63D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: SGRA1R, sgraIR / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q9F6L0, type II site-specific deoxyribonuclease
#2: DNA chain DNA (5'-D(*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*GP*GP*GP*AP*CP*T)-3')


Mass: 4924.192 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*GP*TP*CP*CP*CP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')


Mass: 4875.154 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25 to 21% PEG 4K, 0.1 M HEPES buffer, 0.15-0.20 M NaCl, 0.05 M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 4K11
2HEPES11
3NaCl11
4MgCl211
5PEG 4K12
6HEPES12
7NaCl12
8MgCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 8, 2008
Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.95→84.21 Å / Num. obs: 19842 / % possible obs: 97.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 3.4 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 6.6
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2 / Rsym value: 0.392 / % possible all: 96.2

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→50.349 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.46 / σ(F): 1.36 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2815 960 4.84 %
Rwork0.1893 --
obs0.1938 19834 97.29 %
all-20395 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.342 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.4 Å2-0 Å20 Å2
2---8.0806 Å20 Å2
3---15.4806 Å2
Refinement stepCycle: LAST / Resolution: 2.95→50.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 650 2 79 5975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086192
X-RAY DIFFRACTIONf_angle_d1.3478567
X-RAY DIFFRACTIONf_dihedral_angle_d21.7832319
X-RAY DIFFRACTIONf_chiral_restr0.076947
X-RAY DIFFRACTIONf_plane_restr0.0051002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.10550.36231290.23692583X-RAY DIFFRACTION96
3.1055-3.30010.36081250.22632641X-RAY DIFFRACTION96
3.3001-3.55480.2941420.20132648X-RAY DIFFRACTION97
3.5548-3.91240.27061290.18342712X-RAY DIFFRACTION98
3.9124-4.47820.22491450.16012721X-RAY DIFFRACTION99
4.4782-5.64090.26431500.15522729X-RAY DIFFRACTION98
5.6409-50.3560.22461400.16822840X-RAY DIFFRACTION97

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