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- PDB-3n7b: SgrAI bound to secondary site DNA and Ca(II) -

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Basic information

Entry
Database: PDB / ID: 3n7b
TitleSgrAI bound to secondary site DNA and Ca(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: 2.65 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 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
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_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)85,8037
Polymers85,6834
Non-polymers1203
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10250 Å2
ΔGint-87 kcal/mol
Surface area28770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.682, 133.662, 64.748
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: 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.74 Å3/Da / Density % sol: 55.18 %
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 CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 4K11
2HEPES11
3NaCl11
4CaCl211
5PEG 4K12
6HEPES12
7NaCl12
8CaCl212

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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: 2.65→84.324 Å / Num. all: 28125 / Num. obs: 28125 / % possible obs: 99.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 4.3 % / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 10.1
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2 / Rsym value: 0.383 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0031refinement
SCALA3.2.25data scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
PHASERphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→84.32 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.833 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24776 1362 4.8 %RANDOM
Rwork0.17255 ---
obs0.17617 26722 100 %-
all-28132 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.252 Å2
Baniso -1Baniso -2Baniso -3
1--1.93 Å20 Å20 Å2
2---0.08 Å20 Å2
3---2.01 Å2
Refine analyzeLuzzati sigma a free: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.65→84.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5264 650 3 395 6312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226844
X-RAY DIFFRACTIONr_bond_other_d0.0010.024299
X-RAY DIFFRACTIONr_angle_refined_deg1.6832.2029559
X-RAY DIFFRACTIONr_angle_other_deg1.002310441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2235666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15323.132265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.35615868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8871556
X-RAY DIFFRACTIONr_chiral_restr0.0830.21057
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021291
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6831.53342
X-RAY DIFFRACTIONr_mcbond_other0.1141.51346
X-RAY DIFFRACTIONr_mcangle_it1.29725378
X-RAY DIFFRACTIONr_scbond_it1.74833502
X-RAY DIFFRACTIONr_scangle_it2.8554.54180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 106 -
Rwork0.256 1936 -
obs--100 %

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