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- PDB-5tgx: Restriction/modification system-Type II R-SwaI complexed with par... -

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Basic information

Entry
Database: PDB / ID: 5tgx
TitleRestriction/modification system-Type II R-SwaI complexed with partially cleaved DNA
Components
  • (DNA (26-MER)) x 2
  • R-SwaI protein
KeywordsDNA BINDING PROTEIN / R-SwaI / uncleaved DNA complex / R/M system / rare cutter
Function / homology: / SwaI restriction endonuclease / metal ion binding / ACETATE ION / DNA / DNA (> 10) / R-SwaI protein
Function and homology information
Biological speciesStaphylococcus warneri (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsShen, B.W. / Stoddard, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM105691 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target.
Authors: Shen, B.W. / Heiter, D.F. / Lunnen, K.D. / Wilson, G.G. / Stoddard, B.L.
History
DepositionSep 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: R-SwaI protein
B: R-SwaI protein
C: R-SwaI protein
D: R-SwaI protein
H: DNA (26-MER)
I: DNA (26-MER)
J: DNA (26-MER)
K: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,32819
Polymers141,7368
Non-polymers59211
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28910 Å2
ΔGint-156 kcal/mol
Surface area51400 Å2
2
A: R-SwaI protein
B: R-SwaI protein
H: DNA (26-MER)
I: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,31712
Polymers70,8684
Non-polymers4508
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14030 Å2
ΔGint-74 kcal/mol
Surface area26170 Å2
MethodPISA
3
C: R-SwaI protein
D: R-SwaI protein
J: DNA (26-MER)
K: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0107
Polymers70,8684
Non-polymers1423
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13770 Å2
ΔGint-86 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.856, 57.058, 112.785
Angle α, β, γ (deg.)90.00, 108.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17H
27I
18H
28J
19H
29K
110I
210J
111I
211K
112J
212K

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNILEILEAA2 - 2262 - 226
21ASNASNILEILEBB2 - 2262 - 226
12ASNASNILEILEAA2 - 2262 - 226
22ASNASNILEILECC2 - 2262 - 226
13ASNASNILEILEAA2 - 2262 - 226
23ASNASNILEILEDD2 - 2262 - 226
14ASNASNILEILEBB2 - 2262 - 226
24ASNASNILEILECC2 - 2262 - 226
15ASNASNILEILEBB2 - 2262 - 226
25ASNASNILEILEDD2 - 2262 - 226
16ASNASNILEILECC2 - 2262 - 226
26ASNASNILEILEDD2 - 2262 - 226
17DGDGDGDGHE6 - 366 - 26
27DGDGDGDGIF6 - 356 - 25
18DGDGDGDGHE2 - 362 - 26
28DGDGDGDGJG2 - 362 - 26
19DGDGDGDGHE6 - 366 - 26
29DGDGDGDGKH6 - 356 - 25
110DGDGDCDCIF6 - 366 - 26
210DGDGDCDCJG6 - 356 - 25
111DCDCDCDCIF2 - 372 - 27
211DCDCDCDCKH2 - 372 - 27
112DGDGDGDGJG6 - 366 - 26
212DGDGDGDGKH6 - 356 - 25

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
R-SwaI protein


Mass: 27135.119 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SeMet incorporated / Source: (gene. exp.) Staphylococcus warneri (bacteria) / Plasmid: pHKT7 / Cell line (production host): ER2566 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1S4NYF7*PLUS

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DNA chain , 2 types, 4 molecules HJIK

#2: DNA chain DNA (26-MER)


Mass: 8423.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 8174.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 223 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsThe DNA strands are partially cleaved, thus the alternate conformations: A conformer (cleaved) and ...The DNA strands are partially cleaved, thus the alternate conformations: A conformer (cleaved) and B conformer (uncleaved)
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 24 - 28% PEG1000, 100 mM TrisHCl, 5 mM CaCl2, / PH range: 8 - 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9794 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Dec 13, 2013
RadiationMonochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 53972 / % possible obs: 96.1 % / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 30.46 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 12.5
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.613 / % possible all: 79.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→49 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 20.475 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.249 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24197 2971 5.2 %RANDOM
Rwork0.19767 ---
obs0.19992 53972 95.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.234 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20.99 Å2
2---0.75 Å20 Å2
3---1.34 Å2
Refinement stepCycle: 1 / Resolution: 2.3→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7541 2149 32 212 9934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01710365
X-RAY DIFFRACTIONr_bond_other_d0.010.028714
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.74414424
X-RAY DIFFRACTIONr_angle_other_deg1.691320245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7755908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.05625.11409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27151461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4981536
X-RAY DIFFRACTIONr_chiral_restr0.1120.21421
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0210043
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022374
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_it1.942.9163621
X-RAY DIFFRACTIONr_mcbond_other1.9322.9143619
X-RAY DIFFRACTIONr_mcangle_it3.0474.3654526
X-RAY DIFFRACTIONr_mcangle_other3.0474.3654527
X-RAY DIFFRACTIONr_scbond_it2.5173.496744
X-RAY DIFFRACTIONr_scbond_other2.5173.4916745
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9415.1719897
X-RAY DIFFRACTIONr_long_range_B_refined6.37527.912284
X-RAY DIFFRACTIONr_long_range_B_other6.37527.90412285
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A277380.07
12B277380.07
21A273200.08
22C273200.08
31A276420.07
32D276420.07
41B272080.09
42C272080.09
51B273260.08
52D273260.08
61C273900.09
62D273900.09
71H29100.02
72I29100.02
81H36920.11
82J36920.11
91H29080.04
92K29080.04
101I28440.07
102J28440.07
111I39220.11
112K39220.11
121J28360.08
122K28360.08
LS refinement shellResolution: 2.296→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 126 -
Rwork0.331 2818 -
obs--67.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9849-0.7213-0.36631.61670.02694.0405-0.07890.00850.1928-0.09710.05390.0407-0.3863-0.2930.0250.0591-0.0147-0.02170.22750.02280.0215.293136.436433.7589
23.1594-0.0033-0.45341.4719-0.3812.497-0.06420.1579-0.0652-0.2043-0.0727-0.2290.10110.59320.13690.0932-0.00040.03940.44110.01780.039628.374127.689122.8719
33.4119-0.2985-0.80221.5253-0.03763.3692-0.0485-0.07260.05680.21880.19350.2833-0.1524-0.5384-0.1450.10490.11220.03880.47770.03450.0615-9.252530.636384.8421
42.60350.1354-0.29921.1496-0.66134.6891-0.0942-0.04550.12170.23840.0455-0.0953-0.68210.59350.04870.14250.0017-0.04420.4039-0.0840.034414.973635.779474.0712
54.18790.08690.10015.8871-0.1345.94030.05910.3026-0.5463-0.02040.01220.37850.52170.1657-0.07120.0563-0.01840.00170.1617-0.09660.120711.936124.507926.9378
65.7038-0.0181.65012.78740.52326.27180.16250.2347-0.5792-0.08610.06560.35420.6240.0395-0.22810.0886-0.051-0.01030.1465-0.09410.153112.869524.030526.0004
75.01530.12351.50013.5132-1.0396.09930.0395-0.3092-0.56270.17160.2539-0.30850.32290.0911-0.29330.0790.12350.00120.30930.04270.146.302623.638684.1953
83.08140.48110.53335.01780.53356.65660.1025-0.3195-0.58430.24490.0282-0.38390.56950.0572-0.13070.09510.0729-0.00820.22490.0790.15516.484723.566281.6251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 226
2X-RAY DIFFRACTION2B2 - 226
3X-RAY DIFFRACTION3C2 - 226
4X-RAY DIFFRACTION4D2 - 226
5X-RAY DIFFRACTION5H2 - 37
6X-RAY DIFFRACTION6I2 - 37
7X-RAY DIFFRACTION7J1 - 37
8X-RAY DIFFRACTION8K2 - 37

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