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- PDB-5iff: Crystal structure of R.PabI-nonspecific DNA complex -

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Basic information

Entry
Database: PDB / ID: 5iff
TitleCrystal structure of R.PabI-nonspecific DNA complex
Components
  • DNA (5'-D(*GP*CP*AP*CP*TP*AP*GP*TP*TP*CP*GP*AP*AP*CP*TP*AP*GP*TP*GP*C)-3')
  • Uncharacterized protein
KeywordsHYDROLASE/DNA / Restriction enzyme / 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: 1.9 Å
AuthorsWang, D. / Miyazono, K. / Tanokura, M.
CitationJournal: Sci Rep / Year: 2016
Title: Tetrameric structure of the restriction DNA glycosylase R.PabI in complex with nonspecific double-stranded DNA.
Authors: Wang, D. / Miyazono, K.I. / Tanokura, M.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 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: Uncharacterized protein
B: Uncharacterized protein
C: DNA (5'-D(*GP*CP*AP*CP*TP*AP*GP*TP*TP*CP*GP*AP*AP*CP*TP*AP*GP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)56,6423
Polymers56,6423
Non-polymers00
Water2,918162
1
A: Uncharacterized protein
B: Uncharacterized protein
C: DNA (5'-D(*GP*CP*AP*CP*TP*AP*GP*TP*TP*CP*GP*AP*AP*CP*TP*AP*GP*TP*GP*C)-3')

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


Theoretical massNumber of molelcules
Total (without water)113,2846
Polymers113,2846
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area13800 Å2
ΔGint-78 kcal/mol
Surface area45190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.893, 261.716, 65.083
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-122-

HOH

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Components

#1: Protein Uncharacterized protein / R.PabI


Mass: 25254.086 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 8-226 / Mutation: R32A, E63A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Strain: GE5 / Orsay / Gene: PAB0105 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V2B6
#2: DNA chain DNA (5'-D(*GP*CP*AP*CP*TP*AP*GP*TP*TP*CP*GP*AP*AP*CP*TP*AP*GP*TP*GP*C)-3')


Mass: 6133.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M calcium acetate, 0.1M imidazole (pH 8.0), 10% PEG 8000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→43.62 Å / Num. obs: 49388 / % possible obs: 99.6 % / Redundancy: 13.9 % / Biso Wilson estimate: 36.77 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.015 / Rrim(I) all: 0.054 / Net I/σ(I): 28.5 / Num. measured all: 685056
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.9490.11752797131100.7760.411.247299.2
9.11-43.628.80.02831333580.9990.010.0371.268.5

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVY

2dvy


Resolution: 1.9→43.619 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.83
RfactorNum. reflection% reflection
Rfree0.2481 2444 4.96 %
Rwork0.2062 --
obs0.2083 49246 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 170.78 Å2 / Biso mean: 60.99 Å2 / Biso min: 25.51 Å2
Refinement stepCycle: final / Resolution: 1.9→43.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3475 407 0 162 4044
Biso mean---53.7 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134000
X-RAY DIFFRACTIONf_angle_d1.2965485
X-RAY DIFFRACTIONf_chiral_restr0.063613
X-RAY DIFFRACTIONf_plane_restr0.006624
X-RAY DIFFRACTIONf_dihedral_angle_d16.6851553
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.93880.341460.34072677282399
1.9388-1.9810.35991430.289927622905100
1.981-2.0270.32031370.27327432880100
2.027-2.07770.28411410.255527232864100
2.0777-2.13390.261230.244727382861100
2.1339-2.19670.28461500.235127382888100
2.1967-2.26760.27841590.240927412900100
2.2676-2.34860.26191420.24432726286899
2.3486-2.44270.22971320.229627542886100
2.4427-2.55380.28161270.237527582885100
2.5538-2.68840.31621460.246927652911100
2.6884-2.85690.27971570.245727362893100
2.8569-3.07740.24971470.228327842931100
3.0774-3.3870.24811440.20382766291099
3.387-3.87680.25741710.186927872958100
3.8768-4.88330.20391410.156428292970100
4.8833-43.63080.21131380.18542775291393
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)
11.0343-0.78171.54323.4318-1.06245.68420.1361-0.02490-0.2787-0.03980.1019-0.0804-0.1987-0.09030.29010.05480.08430.3378-0.00590.2119-24.3926-57.61184.8182
21.2009-1.5456-0.05498.855-0.5088-0.0003-0.08050.19080.31020.00420.111-1.4604-0.3369-0.0095-0.03270.3722-0.05810.05860.44370.03430.5171-6.196-37.30210.5346
32.4694-0.29441.32042.0022-0.2716.07420.1339-0.01550.0926-0.1003-0.0061-0.0125-0.3063-0.1574-0.06260.26050.06530.09450.29760.00810.2016-21.2587-55.60477.692
43.61021.1896-1.26336.857-2.15725.79650.5346-0.20830.67290.4183-0.18460.4884-1.06530.1023-0.21240.6581-0.1070.13290.4165-0.02850.6061-19.9749-15.078619.4712
51.61810.0849-1.59855.943-0.34452.61320.20580.34020.1533-1.261-0.2513-0.481-0.2527-0.11150.01170.4122-0.03030.09110.4130.02260.449-7.9226-36.60735.0574
63.3798-2.6042-3.99083.27461.5046.79980.67130.0090.21560.2213-0.68880.0068-0.173-0.27430.10010.482-0.04270.05810.45340.09390.511-16.32-24.071113.6859
73.24471.0273-2.32235.4987-3.30413.97590.8191-0.42410.75210.1356-0.44170.2545-1.0780.2103-0.22720.6617-0.10580.11720.42550.00410.6774-19.2866-13.608817.0527
88.8836-0.4296-5.93412.86660.59843.93960.22220.14430.16460.65780.27860.04760.4307-0.0906-0.45240.6756-0.13410.03630.4579-0.05340.3236-35.9668-33.7432.0831
93.8912-3.43972.80357.8667-5.77424.2655-0.074-0.20590.2756-0.84490.5261-0.15150.1262-0.3003-0.44120.53490.04360.0470.5372-0.05090.2681-37.8119-34.18990.2916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 105 )A8 - 105
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 140 )A106 - 140
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 223 )A141 - 223
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 105 )B8 - 105
5X-RAY DIFFRACTION5chain 'B' and (resid 106 through 140 )B106 - 140
6X-RAY DIFFRACTION6chain 'B' and (resid 141 through 172 )B141 - 172
7X-RAY DIFFRACTION7chain 'B' and (resid 173 through 223 )B173 - 223
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 10 )C1 - 10
9X-RAY DIFFRACTION9chain 'C' and (resid 11 through 20 )C11 - 20

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