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- PDB-6l2o: Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-5bp-GTAC) ... -

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Basic information

Entry
Database: PDB / ID: 6l2o
TitleCrystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-5bp-GTAC) complex
Components
  • DNA (5'-D(*CP*A*GP*CP*AP*GP*TP*AP*CP*TP*TP*AP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*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: 2.2 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(*CP*A*GP*CP*AP*GP*TP*AP*CP*TP*TP*AP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*G)-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(*CP*A*GP*CP*AP*GP*TP*AP*CP*TP*TP*AP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*G)-3')

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


Theoretical massNumber of molelcules
Total (without water)115,4266
Polymers115,4266
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area14660 Å2
ΔGint-83 kcal/mol
Surface area43560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.429, 82.429, 140.345
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(*CP*A*GP*CP*AP*GP*TP*AP*CP*TP*TP*AP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*G)-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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 0.1 M Bis-Tris pH 6.3, 51% MPD

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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 PILATUS3 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: 2.2→46.78 Å / Num. obs: 28711 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 54.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.023 / Rrim(I) all: 0.074 / Net I/σ(I): 14.4
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
2.2-2.276.70.8521640424490.8320.3490.9241.799.9
9.07-46.788.80.04841754770.9990.0170.0513899.3

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFF

5iff


Resolution: 2.2→41.21 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0.36 / Phase error: 32.8
RfactorNum. reflection% reflection
Rfree0.2572 2677 4.96 %
Rwork0.2166 --
obs0.2186 28609 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 173.72 Å2 / Biso mean: 82.3083 Å2 / Biso min: 39.09 Å2
Refinement stepCycle: final / Resolution: 2.2→41.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 407 0 0 3901
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044018
X-RAY DIFFRACTIONf_angle_d0.6235507
X-RAY DIFFRACTIONf_chiral_restr0.046615
X-RAY DIFFRACTIONf_plane_restr0.003629
X-RAY DIFFRACTIONf_dihedral_angle_d10.2562382
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.240.3681340.3674263499
2.24-2.28310.41731420.33842746100
2.2831-2.32970.35941090.33252719100
2.3297-2.38030.35821480.30572718100
2.3803-2.43570.35491540.30782686100
2.4357-2.49660.39591260.30052713100
2.4966-2.56410.38271380.28312717100
2.5641-2.63950.26921960.2942611100
2.6395-2.72470.33371300.2777269399
2.7247-2.82210.3031300.27032720100
2.8221-2.93510.30861200.27342726100
2.9351-3.06860.31051680.26922696100
3.0686-3.23030.27721310.25582684100
3.2303-3.43260.2565930.22412780100
3.4326-3.69750.25721640.22282697100
3.6975-4.06930.21051420.20282704100
4.0693-4.65740.22561760.16562653100
4.6574-5.86520.24141540.17422707100
5.8652-41.2140.21181220.18062721100
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)
15.2487-4.2828-3.90325.99636.81867.95020.3987-0.03460.3505-0.5094-0.1986-0.3568-0.4691-0.7512-0.17990.65080.0370.02230.50440.03990.411738.0872-20.3744-38.0982
24.75183.21310.38942.20860.0446.42490.0327-0.090.83440.39440.2339-0.1162-1.22460.8548-0.36790.8405-0.020.13240.7692-0.09070.596944.4777-7.6797-29.6903
30.9324-0.3026-0.75472.21892.30745.3235-0.0003-0.1056-0.0620.2438-0.0374-0.06440.69140.17150.01030.4810.0139-0.04130.58320.04390.404942.1664-27.2197-19.0351
42.2691-0.87280.26753.12640.17543.93010.1059-0.25660.1124-0.1107-0.04680.0878-0.0742-0.2102-0.07480.41780.0373-0.03020.5628-0.04180.319941.3241-24.5099-27.409
54.4815-2.3513-1.69038.93315.34023.20740.11790.35860.3009-1.3194-0.40980.0075-1.3618-1.06720.45470.7340.4478-0.22521.2573-0.07570.579712.4748-5.9975-8.956
63.87111.32510.2666.05910.65815.9461-0.0640.23920.1217-0.25280.36950.5935-0.6595-1.2157-0.2340.44790.1683-0.01940.98110.0340.417817.4591-7.6359-4.3928
73.0608-2.8598-2.40026.6273.53617.03310.3225-0.16640.73680.0810.1992-0.8922-1.20890.6913-0.56420.7238-0.21860.01730.70960.0890.451440.5282-3.9102-3.3117
84.5569-1.78931.94972.28-0.30174.91130.26930.63140.1248-0.3634-0.3841-0.0998-0.7481-0.32270.06350.61060.02230.00230.49820.00370.350130.9454-8.0623-5.1653
92.63880.48720.70795.4081.41474.95330.31690.08310.2877-0.029-0.27530.5307-1.1075-1.2150.04680.72150.27210.04640.85580.00410.400219.1675-0.5381-2.503
103.0062-3.0464-3.33623.11073.80759.89571.73850.847-1.61760.8798-1.67172.44-0.5706-0.53210.24151.28960.2203-0.08551.39530.29421.386821.5406-6.6259-33.5926
113.4651.9557-3.69696.6716-5.10536.6194-1.87080.4597-1.0616-1.34591.0414-0.30951.4678-1.26590.59640.6505-0.0777-0.03770.93480.1760.882919.7455-19.6372-21.0845
127.47940.49250.20842.2814-0.5776.0514-1.141-1.9313-0.3497-0.09910.3779-0.0095-0.91-1.1360.91720.8966-0.0702-0.24481.19750.21330.87220.1337-20.3478-24.1361
131.92232.8473-2.37354.2932-3.13024.43981.0210.743911.8405-0.09840.9188-1.5938-2.6759-0.59091.3280.30230.09191.72880.10390.984-10.812-25.767-12.5079
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 30 )A7 - 30
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 66 )A31 - 66
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 145 )A67 - 145
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 223 )A146 - 223
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 30 )B7 - 30
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 92 )B31 - 92
7X-RAY DIFFRACTION7chain 'B' and (resid 93 through 129 )B93 - 129
8X-RAY DIFFRACTION8chain 'B' and (resid 130 through 172 )B130 - 172
9X-RAY DIFFRACTION9chain 'B' and (resid 173 through 223 )B173 - 223
10X-RAY DIFFRACTION10chain 'C' and (resid -9 through -5 )C-9 - -5
11X-RAY DIFFRACTION11chain 'C' and (resid -4 through 0 )C-4 - 0
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 5 )C1 - 5
13X-RAY DIFFRACTION13chain 'C' and (resid 6 through 10 )C6 - 10

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