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- PDB-6l2n: Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-3bp-GTAC) ... -

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Basic information

Entry
Database: PDB / ID: 6l2n
TitleCrystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-3bp-GTAC) complex
Components
  • DNA (5'-D(*TP*CP*AP*GP*CP*AP*GP*TP*AP*CP*TP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*GP*A)-3')
  • RE_R_Pab1 domain-containing protein
KeywordsHYDROLASE/DNA / glycosylase / complex / HYDROLASE / HYDROLASE-DNA complex
Function / homologyRestriction endonuclease, type II, Pab1 / R.Pab1 restriction endonuclease / DNA / DNA (> 10) / Restriction endonuclease type II Pab1 domain-containing protein
Function and homology information
Biological speciesPyrococcus abyssi (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMiyazono, K. / Wang, D. / Ito, T. / Tanokura, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science26712012 Japan
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI.
Authors: Miyazono, K.I. / Wang, D. / Ito, T. / Tanokura, M.
History
DepositionOct 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RE_R_Pab1 domain-containing protein
B: RE_R_Pab1 domain-containing protein
C: DNA (5'-D(*TP*CP*AP*GP*CP*AP*GP*TP*AP*CP*TP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)57,7133
Polymers57,7133
Non-polymers00
Water00
1
A: RE_R_Pab1 domain-containing protein
B: RE_R_Pab1 domain-containing protein
C: DNA (5'-D(*TP*CP*AP*GP*CP*AP*GP*TP*AP*CP*TP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*GP*A)-3')

A: RE_R_Pab1 domain-containing protein
B: RE_R_Pab1 domain-containing protein
C: DNA (5'-D(*TP*CP*AP*GP*CP*AP*GP*TP*AP*CP*TP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)115,4266
Polymers115,4266
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area14380 Å2
ΔGint-82 kcal/mol
Surface area45910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.682, 83.682, 140.346
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RE_R_Pab1 domain-containing protein


Mass: 25324.137 Da / Num. of mol.: 2 / Mutation: Y68F,K154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / Gene: PAB0105 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V2B6
#2: DNA chain DNA (5'-D(*TP*CP*AP*GP*CP*AP*GP*TP*AP*CP*TP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*GP*A)-3')


Mass: 7064.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.1 M Bis-Tris pH 5.9, 51% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.45→41.84 Å / Num. obs: 20923 / % possible obs: 97.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 62.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.023 / Rrim(I) all: 0.05 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.45-2.554.50.691925420580.8660.3540.7811.986.8
8.84-41.844.30.02421865070.9990.0130.02745.396.9

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.12refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFF

5iff


Resolution: 2.45→41.84 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0.51 / Phase error: 34.05
RfactorNum. reflection% reflection
Rfree0.2557 1980 5.06 %
Rwork0.2288 --
obs0.2303 20891 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 180.83 Å2 / Biso mean: 84.8186 Å2 / Biso min: 40.92 Å2
Refinement stepCycle: final / Resolution: 2.45→41.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3483 469 0 0 3952
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034077
X-RAY DIFFRACTIONf_angle_d0.6025602
X-RAY DIFFRACTIONf_chiral_restr0.043626
X-RAY DIFFRACTIONf_plane_restr0.003631
X-RAY DIFFRACTIONf_dihedral_angle_d10.92403
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4504-2.51170.4683980.3837216779
2.5117-2.57960.30141820.3618253495
2.5796-2.65550.39821440.3726270999
2.6555-2.74120.31971230.34042758100
2.7412-2.83920.37881500.3194272399
2.8392-2.95280.31221260.3309271598
2.9528-3.08720.2951380.3065269397
3.0872-3.24990.30521250.2883269499
3.2499-3.45340.23351260.2564274999
3.4534-3.71990.29231220.2273270598
3.7199-4.09390.30831350.2223269298
4.0939-4.68560.21651780.1808268698
4.6856-5.90080.22321610.1832264798
5.9008-41.840.20741720.1781265697
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)
12.01140.14986.95817.12551.9455.1659-2.613-1.3273-0.6522-1.78192.3368-0.14370.50170.99260.64811.3855-0.15320.50520.9671-0.02321.1669.9513-17.8885-13.6084
28.66644.7625-2.02127.9228-5.03093.3877-0.8196-0.20020.327-0.93310.29150.06281.05620.47080.38680.72350.02590.14660.9250.01910.8509-1.6476-29.5465-3.7022
37.948-5.41475.44255.7025-1.50835.5827-0.61730.1023-2.20312.19930.49890.9526-1.3343-0.30380.15360.81090.22130.05621.03880.17250.9826-12.9515-16.75542.3992
45.7957-2.1686-4.79859.25963.35766.39610.9706-0.78030.98510.32010.104-0.982-1.5550.9107-0.81431.0345-0.06220.01320.8994-0.24460.8214-25.9813-4.72949.5473
58.36045.82361.7544.51030.50755.42890.0020.04870.3548-0.0720.19390.07540.0723-0.6379-0.13720.54590.0281-0.00040.56980.0470.40251.0248-43.9954-14.9867
64.38742.55960.12324.36461.29375.18730.2092-0.14840.21920.22820.015-0.18440.23710.3935-0.27280.5550.0295-0.00160.45820.01360.34544.5636-45.7985-8.1329
70.23150.04771.12972.23572.89467.47540.1484-0.2616-0.14620.3632-0.0382-0.01240.7506-0.2005-0.09830.7616-0.004-0.02660.51730.07790.38161.1857-51.195611.4464
83.80980.3486-0.54482.242-0.72594.39860.0919-0.02990.10250.03270.1558-0.05270.1821-0.1555-0.23930.5691-0.0105-0.03360.4219-0.00290.3355-0.8001-48.6989-4.1574
94.76240.3399-0.72933.04451.78621.38970.27631.2920.67190.2569-0.10640.502-2.1597-0.1546-0.13931.8020.1776-0.00570.66650.16510.54431.1748-14.052714.0723
100.8169-1.63371.07113.3907-2.40886.7790.46350.4436-0.2953-0.0004-0.06240.5461-0.7027-1.2398-0.43310.81530.1505-0.06450.8190.00170.5785-5.9395-29.310418.0514
112.6036-0.33560.18482.32010.64480.2160.4019-0.1089-0.44490.210.76080.349-0.7678-1.9785-0.98511.32710.67970.11991.22050.12050.8399-14.6179-21.747319.176
126.48430.08621.72262.44730.3274.9695-0.54250.40080.3789-0.51970.5242-0.097-0.88080.0668-0.21351.15160.17790.12680.59050.0430.51996.1841-19.41916.641
134.2672-2.426-2.33761.46311.7012.65410.6252-0.5082.3066-0.72690.8019-0.3224-3.58471.1846-0.76472.7244-0.55350.32070.7126-0.21870.832116.6304-8.77423.1702
148.52470.52214.11287.0969-1.33832.43960.0403-1.805-0.24341.43481.17030.1715-0.87081.1245-1.32421.3884-0.37160.1691.5784-0.07710.619725.8402-19.095629.4015
154.7264.42892.85988.08823.58747.48330.1153-0.4156-0.8751-0.6550.1458-1.21530.49250.6226-0.25710.55690.18870.07210.60140.00890.516312.0013-47.971914.5657
161.20940.05810.32259.82193.30769.92360.2701-0.03790.04460.5295-0.534-0.2696-0.2862-0.1130.18620.4764-0.0362-0.02080.52930.08530.38597.5504-34.854422.6128
175.19530.09820.44032.57382.51142.5289-0.32421.0786-0.0702-0.93040.493-0.6501-0.19091.45570.11781.03650.02380.15880.8587-0.02530.564712.9364-32.524111.8244
182.7048-4.00530.11597.45330.33627.67430.52130.5664-0.1694-1.1371-0.0712-0.0315-1.9876-0.0327-0.49440.79160.04690.05450.4686-0.0580.47385.783-25.383418.9861
194.71730.3807-1.65030.9197-1.15742.071-1.46420.17741.23812.27231.61830.4565-2.6911-1.6142-0.32162.20120.78970.18320.7458-0.01440.6877-6.6558-12.325320.082
205.9319-3.5674-0.25359.01940.23383.5869-0.2798-0.78720.20620.48460.56-0.116-1.39440.7944-0.41190.9389-0.24930.03360.76410.04010.472115.5435-21.932824.4226
213.4210.73050.59215.28422.65248.37440.1063-0.50770.2402-0.532-0.1254-0.793-1.05421.0935-0.01761.1347-0.50080.14161.2922-0.08460.595125.1938-19.121618.3965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid -11 through -7 )C-11 - -7
2X-RAY DIFFRACTION2chain 'C' and (resid -6 through -2 )C-6 - -2
3X-RAY DIFFRACTION3chain 'C' and (resid -1 through 3 )C-1 - 3
4X-RAY DIFFRACTION4chain 'C' and (resid 4 through 11 )C4 - 11
5X-RAY DIFFRACTION5chain 'A' and (resid 7 through 30 )A7 - 30
6X-RAY DIFFRACTION6chain 'A' and (resid 31 through 92 )A31 - 92
7X-RAY DIFFRACTION7chain 'A' and (resid 93 through 145 )A93 - 145
8X-RAY DIFFRACTION8chain 'A' and (resid 146 through 223 )A146 - 223
9X-RAY DIFFRACTION9chain 'B' and (resid 8 through 30 )B8 - 30
10X-RAY DIFFRACTION10chain 'B' and (resid 31 through 43 )B31 - 43
11X-RAY DIFFRACTION11chain 'B' and (resid 44 through 55 )B44 - 55
12X-RAY DIFFRACTION12chain 'B' and (resid 56 through 77 )B56 - 77
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 92 )B78 - 92
14X-RAY DIFFRACTION14chain 'B' and (resid 93 through 105 )B93 - 105
15X-RAY DIFFRACTION15chain 'B' and (resid 106 through 129 )B106 - 129
16X-RAY DIFFRACTION16chain 'B' and (resid 130 through 145 )B130 - 145
17X-RAY DIFFRACTION17chain 'B' and (resid 146 through 159 )B146 - 159
18X-RAY DIFFRACTION18chain 'B' and (resid 160 through 172 )B160 - 172
19X-RAY DIFFRACTION19chain 'B' and (resid 173 through 193 )B173 - 193
20X-RAY DIFFRACTION20chain 'B' and (resid 194 through 208 )B194 - 208
21X-RAY DIFFRACTION21chain 'B' and (resid 209 through 223 )B209 - 223

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