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- PDB-5th3: Restriction/modification system-Type II R.SwaI cleaved DNA complex -

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Basic information

Entry
Database: PDB / ID: 5th3
TitleRestriction/modification system-Type II R.SwaI cleaved DNA complex
Components
  • (DNA (cleaved 25-MER, portion ...) x 2
  • (DNA (cleaved 26-MER, portion ...) x 2
  • R-SwaI protein
KeywordsDNA BINDING PROTEIN / I-SwaI / cleaved DNA complex / R/M system
Function / homologymetal ion binding / ACETATE ION / DNA / DNA (> 10) / R-SwaI protein
Function and homology information
Biological speciesStaphylococcus warneri (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 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 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._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 1.4Apr 3, 2024Group: 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
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_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.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

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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 (cleaved 25-MER, portion 1)
h: DNA (cleaved 25-MER, portion 2)
I: DNA (cleaved 26-MER, portion 1)
i: DNA (cleaved 26-MER, portion 2)
J: DNA (cleaved 25-MER, portion 1)
j: DNA (cleaved 25-MER, portion 2)
K: DNA (cleaved 26-MER, portion 1)
k: DNA (cleaved 26-MER, portion 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,94722
Polymers141,55612
Non-polymers39110
Water2,396133
1
A: R-SwaI protein
B: R-SwaI protein
H: DNA (cleaved 25-MER, portion 1)
h: DNA (cleaved 25-MER, portion 2)
I: DNA (cleaved 26-MER, portion 1)
i: DNA (cleaved 26-MER, portion 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,03412
Polymers70,7786
Non-polymers2566
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13970 Å2
ΔGint-95 kcal/mol
Surface area25820 Å2
MethodPISA
2
C: R-SwaI protein
D: R-SwaI protein
J: DNA (cleaved 25-MER, portion 1)
j: DNA (cleaved 25-MER, portion 2)
K: DNA (cleaved 26-MER, portion 1)
k: DNA (cleaved 26-MER, portion 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,91310
Polymers70,7786
Non-polymers1354
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14340 Å2
ΔGint-94 kcal/mol
Surface area26190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.748, 57.072, 113.443
Angle α, β, γ (deg.)90.00, 107.60, 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
210K
111J
211K

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 226
2010B1 - 226
1020A1 - 226
2020C1 - 226
1030A1 - 226
2030D1 - 226
1040B1 - 226
2040C1 - 226
1050B1 - 226
2050D1 - 226
1060C1 - 226
2060D1 - 226
1070H6 - 36
2070I6 - 35
1080H3 - 36
2080J3 - 36
1090H6 - 36
2090K6 - 35
10100I2 - 35
20100K2 - 35
10110J6 - 36
20110K6 - 35

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

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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
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 (cleaved 25-MER, portion ... , 2 types, 4 molecules HJhj

#2: DNA chain DNA (cleaved 25-MER, portion 1)


Mass: 4376.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (cleaved 25-MER, portion 2)


Mass: 4001.612 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA (cleaved 26-MER, portion ... , 2 types, 4 molecules IKik

#4: DNA chain DNA (cleaved 26-MER, portion 1)


Mass: 4232.741 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (cleaved 26-MER, portion 2)


Mass: 3896.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 143 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.28 Å3/Da / Density meas: 45.98 Mg/m3 / Density % sol: 48.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 24-28% PEG1000, 100 mM TrisHCl, 5 mM MgCl2 / PH range: 8 - 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 70 / Detector: CCD / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 56787 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Biso Wilson estimate: 33.9 Å2 / Rsym value: 9.5 / Net I/σ(I): 17.8
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 1.35 / CC1/2: 0.678 / % possible all: 85.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SwaI

Resolution: 2.33→50.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 21.706 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.399 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23891 2894 5.1 %RANDOM
Rwork0.19846 ---
obs0.20051 53845 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.98 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å2-0.64 Å2
2--4.16 Å20 Å2
3----1.97 Å2
Refinement stepCycle: 1 / Resolution: 2.33→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7576 2127 22 133 9858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01710245
X-RAY DIFFRACTIONr_bond_other_d0.010.028714
X-RAY DIFFRACTIONr_angle_refined_deg2.1271.76414224
X-RAY DIFFRACTIONr_angle_other_deg1.746320247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.835926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16925.074406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29151458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2851536
X-RAY DIFFRACTIONr_chiral_restr0.1150.21405
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0210052
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022356
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_it2.4183.4233672
X-RAY DIFFRACTIONr_mcbond_other2.413.4213670
X-RAY DIFFRACTIONr_mcangle_it3.7455.1264602
X-RAY DIFFRACTIONr_mcangle_other3.7445.1274603
X-RAY DIFFRACTIONr_scbond_it3.3084.0926573
X-RAY DIFFRACTIONr_scbond_other3.3084.0936574
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0076.0589621
X-RAY DIFFRACTIONr_long_range_B_refined7.14532.31312178
X-RAY DIFFRACTIONr_long_range_B_other7.14532.31712179
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)
11A280920.07
12B280920.07
21A275840.09
22C275840.09
31A280800.07
32D280800.07
41B278760.09
42C278760.09
51B278760.07
52D278760.07
61C275420.09
62D275420.09
71H29740.08
72I29740.08
81H36800.09
82J36800.09
91H29980.06
92K29980.06
101I38080.07
102K38080.07
111J29860.04
112K29860.04
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 159 -
Rwork0.334 3438 -
obs--84.54 %
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)
12.7434-0.4581-0.41911.7680.26434.4073-0.08160.08070.1594-0.08140.03470.1228-0.458-0.40680.0470.06310.0172-0.01120.11170.01720.21245.556436.365734.4227
23.55340.3466-0.72351.6132-0.29982.9673-0.03620.1824-0.132-0.1368-0.0682-0.23940.11390.67310.10440.0932-0.00210.07090.366-0.01940.247328.700627.873323.0842
33.6583-0.7243-0.95171.70420.13463.5352-0.0432-0.11740.11040.12680.13870.2295-0.0671-0.5155-0.09560.09290.10520.05630.2732-0.02330.2767-8.605130.7185.7375
42.42950.3378-0.62921.7214-1.06365.4089-0.0448-0.11450.20730.26380.0227-0.1182-0.81270.8170.02210.1799-0.0381-0.0310.3181-0.12430.221715.680735.664774.5384
54.159-0.64930.5155.5177-1.05575.68480.03960.3251-0.3391-0.03890.04890.17680.33760.0214-0.08850.0383-0.02660.06430.0753-0.13470.299512.071125.450726.1558
64.4056-0.19131.66792.23020.20166.92550.0180.1387-0.3634-0.14750.11510.28650.3405-0.266-0.1330.0524-0.07080.05740.1501-0.13360.338111.807725.261323.8438
74.45360.2281.79233.2401-0.90845.9663-0.0036-0.3071-0.40560.11390.1522-0.23280.23790.1651-0.14860.06610.08430.06850.3028-0.03510.30836.947723.787684.9186
83.61351.00761.33533.79771.11596.43060.1071-0.3283-0.42770.18520.025-0.2770.3615-0.0172-0.13210.11460.07930.07350.14510.03890.29247.094823.706982.3278
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 226
2X-RAY DIFFRACTION2B1 - 226
3X-RAY DIFFRACTION3C1 - 226
4X-RAY DIFFRACTION4D1 - 226
5X-RAY DIFFRACTION5H3 - 14
6X-RAY DIFFRACTION5h25 - 37
7X-RAY DIFFRACTION6I1 - 14
8X-RAY DIFFRACTION6i25 - 36
9X-RAY DIFFRACTION7J1 - 14
10X-RAY DIFFRACTION7j25 - 37
11X-RAY DIFFRACTION8K2 - 14
12X-RAY DIFFRACTION8k25 - 37

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