[English] 日本語
Yorodumi
- PDB-6l2n: Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-3bp-GTAC) ... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more