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- PDB-6m3l: Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) complex -

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Basic information

Entry
Database: PDB / ID: 6m3l
TitleCrystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) complex
Components
  • DNA (5'-D(*CP*GP*CP*AP*TP*CP*GP*AP*TP*TP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*GP*CP*G)-3')
  • RE_R_Pab1 domain-containing protein
KeywordsHYDROLASE/DNA / glycosylase / 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: 2.75 Å
AuthorsMiyazono, K. / Wang, D. / Ito, T. / Tanokura, M.
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
DepositionMar 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 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.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
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 29, 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(*CP*GP*CP*AP*TP*CP*GP*AP*TP*TP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)57,7143
Polymers57,7143
Non-polymers00
Water00
1
A: RE_R_Pab1 domain-containing protein
B: RE_R_Pab1 domain-containing protein
C: DNA (5'-D(*CP*GP*CP*AP*TP*CP*GP*AP*TP*TP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*GP*CP*G)-3')

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


Theoretical massNumber of molelcules
Total (without water)115,4286
Polymers115,4286
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Unit cell
Length a, b, c (Å)84.153, 84.153, 140.530
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: Y65F, K151A
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: G8ZFZ3
#2: DNA chain DNA (5'-D(*CP*GP*CP*AP*TP*CP*GP*AP*TP*TP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*GP*CP*G)-3')


Mass: 7065.574 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M Bis-Tris pH 6.0 and 50% MPD

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→46.84 Å / Num. obs: 15362 / % possible obs: 99 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rpim(I) all: 0.035 / Rrim(I) all: 0.064 / Rsym value: 0.053 / Net I/σ(I): 11.8
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 4.3 % / Num. unique obs: 2201 / CC1/2: 0.857 / Rpim(I) all: 0.422 / Rrim(I) all: 0.752 / Rsym value: 0.614 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFF

5iff


Resolution: 2.75→42.076 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 41.91
RfactorNum. reflection% reflection
Rfree0.3065 1307 4.58 %
Rwork0.2833 --
obs0.2844 15237 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 235.09 Å2 / Biso mean: 118.7646 Å2 / Biso min: 51.6 Å2
Refinement stepCycle: final / Resolution: 2.75→42.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 246 0 0 3342
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043431
X-RAY DIFFRACTIONf_angle_d0.6584675
X-RAY DIFFRACTIONf_chiral_restr0.045518
X-RAY DIFFRACTIONf_plane_restr0.003550
X-RAY DIFFRACTIONf_dihedral_angle_d15.0562039
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.75-2.85980.55181100.4513309799
2.8598-2.98990.47331490.3985300999
2.9899-3.14750.31871450.3608302599
3.1475-3.34460.39171760.3456299298
3.3446-3.60280.36881250.2979305098
3.6028-3.96510.35671740.2832299099
3.9651-4.53820.31081380.2472306399
4.5382-5.71540.20881450.2478302299
5.7154-42.0760.28971450.2679297397
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)
16.1124-1.075-0.39434.48454.41634.4390.08411.4250.0358-1.40570.1309-0.2558-0.29150.4668-0.09761.21060.2371-0.08270.88270.01830.515941.5389-25.2981-41.2513
27.70752.23810.77982.05182.52358.5303-0.1228-0.03971.3143-0.2366-0.51930.7043-1.233-0.51920.42881.18410.09260.03450.7056-0.11510.868240.8092-9.8691-27.2639
34.97722.2831-0.75677.9917-0.26127.4193-0.0421-0.02451.3079-0.0311-0.20070.413-1.691.27340.24691.7256-0.0229-0.10161.2635-0.02370.77645.7498-8.3417-32.0897
42.52921.4810.72363.8384-0.25486.4373-0.3262-0.2463-0.41680.13140.12320.12011.64480.26530.23961.18510.3390.14520.74210.03380.424342.1182-37.1476-30.9399
54.2959-2.8262-1.29524.04663.31598.2866-0.0743-0.6230.36290.31070.2039-0.31540.67220.3592-0.02010.84150.0391-0.09691.101-0.0150.433843.3865-18.4681-7.0837
63.94841.2318-0.33735.2817-0.6788.6644-0.1306-0.17610.2082-0.6120.29720.19240.35950.3693-0.13770.91620.3025-0.04540.7355-0.04690.341942.6107-25.2221-27.9914
72.0602-0.37131.78680.2010.23443.4179-0.31270.27990.3964-0.11210.06020.4103-0.6316-1.853-0.15361.11340.2134-0.18543.00830.14270.317620.2996-9.8795-6.2509
80.3818-0.4772-0.38060.58580.46780.37310.23050.07870.622-0.0552-0.16730.4684-0.9546-1.1861-0.05862.0551.63970.362.66330.15871.136615.99879.9007-0.6571
93.1468-0.895-2.04051.92141.42265.3220.5707-0.17520.7175-0.5063-0.65840.1192-2.064-0.4940.11342.89010.51020.14342.2257-0.12920.675529.689212.73255.8357
105.7271-4.9999-4.77215.67415.69975.76590.31490.39110.5617-0.6343-0.7328-0.1178-2.2738-0.00290.42141.3908-0.01050.07191.53050.07310.751844.1009-4.4524-5.7235
112.48830.93071.24032.60844.3987.687-0.1093-0.39590.12170.0813-0.1099-1.9320.69551.99120.251.23570.43830.00681.7030.14390.759953.0674-27.1385-12.9285
124.5359-1.7462-2.60473.26360.68935.0209-0.35270.3109-0.0120.39370.03860.3036-0.2524-1.51470.29940.73270.253-0.06731.4889-0.04870.491134.1299-11.0224-0.6922
133.00160.54660.60562.98340.23283.8912-0.32210.58970.1235-1.33970.14860.0855-0.3787-0.50150.10771.45510.156-0.08372.0028-0.2280.389734.7638-5.765-11.6431
146.21140.6218-1.20653.24781.61181.18350.26971.22640.0375-0.79750.09880.2711-0.9189-1.6218-0.19850.78530.2842-0.07222.23160.1880.65823.0534-6.8067-3.01
152.55680.19420.76020.8829-0.44721.75190.1952-0.20110.07040.24850.26380.3329-0.7878-1.4250.2531.86540.95680.00712.07880.01820.191926.26132.32491.4671
167.4705-4.9184-3.23224.74533.91953.54930.66980.98431.8612-0.23920.38690.1628-2.481-2.388-0.75652.79990.86450.24911.76960.49291.076830.094211.2481-5.7693
175.83494.5024-3.03868.9454-1.23662.7065-0.1589-2.0478-0.6642-1.915-0.8371-1.2584-0.3147-0.06181.06121.8033-0.4082-0.12132.38060.27631.124814.9697-17.8181-24.8586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 23 )A8 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 43 )A24 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 66 )A44 - 66
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 105 )A67 - 105
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 145 )A106 - 145
6X-RAY DIFFRACTION6chain 'A' and (resid 146 through 223 )A146 - 223
7X-RAY DIFFRACTION7chain 'B' and (resid 27 through 77 )B27 - 77
8X-RAY DIFFRACTION8chain 'B' and (resid 78 through 92 )B78 - 92
9X-RAY DIFFRACTION9chain 'B' and (resid 93 through 105 )B93 - 105
10X-RAY DIFFRACTION10chain 'B' and (resid 106 through 119 )B106 - 119
11X-RAY DIFFRACTION11chain 'B' and (resid 120 through 129 )B120 - 129
12X-RAY DIFFRACTION12chain 'B' and (resid 130 through 145 )B130 - 145
13X-RAY DIFFRACTION13chain 'B' and (resid 146 through 159 )B146 - 159
14X-RAY DIFFRACTION14chain 'B' and (resid 160 through 193 )B160 - 193
15X-RAY DIFFRACTION15chain 'B' and (resid 194 through 207 )B194 - 207
16X-RAY DIFFRACTION16chain 'B' and (resid 208 through 222 )B208 - 222
17X-RAY DIFFRACTION17chain 'C' and (resid -7 through 4 )C-7 - 4

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