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- PDB-3mq6: Domain swapped SgrAI with DNA and calcium bound -

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Basic information

Entry
Database: PDB / ID: 3mq6
TitleDomain swapped SgrAI with DNA and calcium bound
Components
  • DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
  • SgraIR restriction enzyme
KeywordsHYDROLASE/DNA / RESTRICTION ENZYME-DNA COMPLEX / HYDROLASE-DNA COMPLEX / DOMAIN SWAPPING
Function / homology
Function and homology information


metal ion binding / identical protein 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 Å
AuthorsDunten, P.W. / Horton, N.C. / Little, E.J.
CitationJournal: Plos Biol. / Year: 2010
Title: Domain swapping in allosteric modulation of DNA specificity.
Authors: Park, C.K. / Joshi, H.K. / Agrawal, A. / Ghare, M.I. / Little, E.J. / Dunten, P.W. / Bitinaite, J. / Horton, N.C.
History
DepositionApr 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 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_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_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_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: SgraIR restriction enzyme
D: SgraIR restriction enzyme
E: SgraIR restriction enzyme
F: SgraIR restriction enzyme
G: SgraIR restriction enzyme
H: SgraIR restriction enzyme
L: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
K: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
N: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
M: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
P: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
O: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
R: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
Q: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,11638
Polymers345,23416
Non-polymers88222
Water24,0501335
1
A: SgraIR restriction enzyme
B: SgraIR restriction enzyme
L: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
K: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,54910
Polymers86,3094
Non-polymers2406
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10500 Å2
ΔGint-118 kcal/mol
Surface area33310 Å2
MethodPISA
2
C: SgraIR restriction enzyme
D: SgraIR restriction enzyme
N: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
M: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,54910
Polymers86,3094
Non-polymers2406
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10620 Å2
ΔGint-117 kcal/mol
Surface area32990 Å2
MethodPISA
3
E: SgraIR restriction enzyme
F: SgraIR restriction enzyme
P: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
O: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5099
Polymers86,3094
Non-polymers2005
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10390 Å2
ΔGint-112 kcal/mol
Surface area33470 Å2
MethodPISA
4
G: SgraIR restriction enzyme
H: SgraIR restriction enzyme
R: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
Q: DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5099
Polymers86,3094
Non-polymers2005
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint-112 kcal/mol
Surface area33240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.384, 134.949, 237.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SgraIR restriction enzyme


Mass: 37941.906 Da / Num. of mol.: 8
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
#2: DNA chain
DNA (5'-D(*AP*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3')


Mass: 5212.386 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: INCLUDES THE SGRAI RECOGNITION SEQUENCE
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1335 / 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: 3.03 Å3/Da / Density % sol: 59.35 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, NACL, HEPES BUFFER, CACL2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2NACLSodium chloride11
3HEPES11
4CACL211
5PEG 400012
6NACLSodium chloride12
7HEPES12
8CACL212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
DetectorDetector: CCD
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 266875 / % possible obs: 94.9 % / Biso Wilson estimate: 33.06 Å2 / Rmerge(I) obs: 0.071

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25.456 Å / SU ML: 0.31 / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 4926 2.02 %RANDOM
Rwork0.2108 ---
obs0.2118 244146 86.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.839 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2591 Å2-0 Å2-0 Å2
2--4.2834 Å2-0 Å2
3----3.0243 Å2
Refinement stepCycle: LAST / Resolution: 2→25.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21089 2747 22 1335 25193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824698
X-RAY DIFFRACTIONf_angle_d1.21934113
X-RAY DIFFRACTIONf_dihedral_angle_d19.99241
X-RAY DIFFRACTIONf_chiral_restr0.0743751
X-RAY DIFFRACTIONf_plane_restr0.0054037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.32141320.27377446X-RAY DIFFRACTION82
2.0227-2.04650.28621380.28796646X-RAY DIFFRACTION73
2.0465-2.07150.44341480.36486306X-RAY DIFFRACTION70
2.0715-2.09770.32141280.30355575X-RAY DIFFRACTION61
2.0977-2.12530.29251690.24737778X-RAY DIFFRACTION86
2.1253-2.15440.3411630.24477977X-RAY DIFFRACTION88
2.1544-2.18510.26781500.25958102X-RAY DIFFRACTION88
2.1851-2.21770.32171240.2756222X-RAY DIFFRACTION87
2.2177-2.25230.55621130.40074733X-RAY DIFFRACTION63
2.2523-2.28920.37481090.3034804X-RAY DIFFRACTION52
2.2892-2.32870.30221570.22838159X-RAY DIFFRACTION90
2.3287-2.3710.27031580.22658207X-RAY DIFFRACTION90
2.371-2.41660.27121990.22728239X-RAY DIFFRACTION90
2.4166-2.46590.29391640.21778421X-RAY DIFFRACTION92
2.4659-2.51940.27831650.22048347X-RAY DIFFRACTION91
2.5194-2.5780.25651810.22628455X-RAY DIFFRACTION92
2.578-2.64240.2941810.22968451X-RAY DIFFRACTION92
2.6424-2.71380.30581810.23398541X-RAY DIFFRACTION93
2.7138-2.79350.29421940.23238611X-RAY DIFFRACTION94
2.7935-2.88360.27751880.22298736X-RAY DIFFRACTION95
2.8836-2.98650.24171700.22138751X-RAY DIFFRACTION95
2.9865-3.10590.25751910.21498843X-RAY DIFFRACTION96
3.1059-3.24690.27591610.20478983X-RAY DIFFRACTION97
3.2469-3.41780.24571770.19538980X-RAY DIFFRACTION97
3.4178-3.63130.23241990.18218976X-RAY DIFFRACTION97
3.6313-3.91080.21931550.17578773X-RAY DIFFRACTION95
3.9108-4.30260.20431700.15928968X-RAY DIFFRACTION96
4.3026-4.92130.18271730.15438884X-RAY DIFFRACTION95
4.9213-6.18560.21291950.17469257X-RAY DIFFRACTION98
6.1856-25.45770.20571930.18049049X-RAY DIFFRACTION94

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