[English] 日本語
Yorodumi
- PDB-8p26: Crystal structure of Arabidopsis thaliana PAXX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p26
TitleCrystal structure of Arabidopsis thaliana PAXX
ComponentsU2 small nuclear ribonucleoprotein auxiliary factor-like protein
KeywordsDNA BINDING PROTEIN / DNA repair / non-homologous end joining / scaffold
Function / homologystomatal closure / response to water deprivation / ribonucleoprotein complex / U2 small nuclear ribonucleoprotein auxiliary factor-like protein
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsOchi, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plant J. / Year: 2023
Title: Plant PAXX has an XLF-like function and stimulates DNA end joining by the Ku-DNA ligase IV/XRCC4 complex.
Authors: Khan, H. / Ochi, T.
History
DepositionMay 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: U2 small nuclear ribonucleoprotein auxiliary factor-like protein
B: U2 small nuclear ribonucleoprotein auxiliary factor-like protein
C: U2 small nuclear ribonucleoprotein auxiliary factor-like protein
D: U2 small nuclear ribonucleoprotein auxiliary factor-like protein
E: U2 small nuclear ribonucleoprotein auxiliary factor-like protein
F: U2 small nuclear ribonucleoprotein auxiliary factor-like protein
G: U2 small nuclear ribonucleoprotein auxiliary factor-like protein
H: U2 small nuclear ribonucleoprotein auxiliary factor-like protein
I: U2 small nuclear ribonucleoprotein auxiliary factor-like protein
J: U2 small nuclear ribonucleoprotein auxiliary factor-like protein


Theoretical massNumber of molelcules
Total (without water)263,44510
Polymers263,44510
Non-polymers00
Water39622
1
A: U2 small nuclear ribonucleoprotein auxiliary factor-like protein
B: U2 small nuclear ribonucleoprotein auxiliary factor-like protein


Theoretical massNumber of molelcules
Total (without water)52,6892
Polymers52,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: U2 small nuclear ribonucleoprotein auxiliary factor-like protein
D: U2 small nuclear ribonucleoprotein auxiliary factor-like protein


Theoretical massNumber of molelcules
Total (without water)52,6892
Polymers52,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: U2 small nuclear ribonucleoprotein auxiliary factor-like protein
F: U2 small nuclear ribonucleoprotein auxiliary factor-like protein


Theoretical massNumber of molelcules
Total (without water)52,6892
Polymers52,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: U2 small nuclear ribonucleoprotein auxiliary factor-like protein
H: U2 small nuclear ribonucleoprotein auxiliary factor-like protein


Theoretical massNumber of molelcules
Total (without water)52,6892
Polymers52,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: U2 small nuclear ribonucleoprotein auxiliary factor-like protein
J: U2 small nuclear ribonucleoprotein auxiliary factor-like protein


Theoretical massNumber of molelcules
Total (without water)52,6892
Polymers52,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.030, 152.419, 187.087
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 through 2 and (name N...
d_2ens_1(chain "B" and ((resid 1 through 2 and (name N...
d_3ens_1(chain "C" and ((resid 1 through 2 and (name N...
d_4ens_1(chain "D" and (resid 1 through 4 or (resid 5...
d_5ens_1(chain "E" and (resid 1 through 16 or (resid 25...
d_6ens_1(chain "F" and ((resid 1 through 2 and (name N...
d_7ens_1(chain "G" and (resid 1 through 4 or (resid 5...
d_8ens_1(chain "H" and ((resid 1 through 2 and (name N...
d_9ens_1(chain "I" and ((resid 1 through 2 and (name N...
d_10ens_1(chain "J" and (resid 1 through 12 or (resid 13...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METPROA1 - 16
d_12ens_1LEUILEA21 - 67
d_13ens_1SERLYSA70 - 138
d_21ens_1METPROB1 - 16
d_22ens_1LEUILEB21 - 67
d_23ens_1SERLYSB70 - 138
d_31ens_1METPROC1 - 16
d_32ens_1LEUGLYC21 - 90
d_33ens_1LYSLYSC92 - 137
d_41ens_1METPROD1 - 16
d_42ens_1LEUILED22 - 68
d_43ens_1SERLYSD71 - 139
d_51ens_1METPROE1 - 16
d_52ens_1LEUILEE19 - 65
d_53ens_1SERLYSE68 - 136
d_61ens_1METPROF1 - 16
d_62ens_1LEUILEF20 - 66
d_63ens_1SERGLYF69 - 91
d_64ens_1LYSLYSF93 - 138
d_71ens_1METPROG1 - 16
d_72ens_1LEUILEG22 - 68
d_73ens_1SERGLYG71 - 93
d_74ens_1LYSLYSG95 - 140
d_81ens_1METILEH1 - 63
d_82ens_1SERGLYH66 - 88
d_83ens_1LYSLYSH90 - 135
d_91ens_1METPROI1 - 16
d_92ens_1LEUILEI20 - 66
d_93ens_1SERLYSI69 - 137
d_101ens_1METPROJ1 - 16
d_102ens_1LEUILEJ22 - 68
d_103ens_1SERGLYJ71 - 93
d_104ens_1LYSLYSJ102 - 147

NCS oper:
IDCodeMatrixVector
1given(0.343224360291, 0.917196423716, 0.202355525811), (0.918902557828, -0.372507061451, 0.129832886381), (0.194461121357, 0.141383200885, -0.970667637654)68.1176928358, -89.5727496846, -46.104794059
2given(-0.216373387047, -0.84861310028, 0.482740472108), (-0.850074433381, 0.406933832017, 0.334332639854), (-0.480162488216, -0.338024647612, -0.809433951917)-75.8329008886, 37.8200334469, -67.8986715648
3given(-0.761342409304, 0.170462018406, -0.625540115482), (0.157348404488, -0.887394837085, -0.433326531291), (-0.62896678402, -0.428337604463, 0.648789396648)-37.8528771309, -71.8247260147, -32.9874355674
4given(0.534249962863, -0.315421666688, -0.784274281973), (0.323953026457, -0.780548633614, 0.534601035552), (-0.78078896882, -0.539678610608, -0.314826274987)-71.0526819316, -95.202697059, -104.231860777
5given(-0.268880791755, 0.517808241312, 0.81214391893), (-0.514700231508, 0.63546114039, -0.575563038024), (-0.814117185368, -0.57276850846, 0.0956527271224)30.5778161183, -30.0485745749, -94.8955411954
6given(-0.957773196618, 0.0434273877986, 0.284226258161), (-0.0100202569265, 0.982885921262, -0.18394254602), (-0.287350131878, -0.179023260428, -0.940946637135)12.3145827305, 29.7601797782, -101.680880462
7given(-0.230046175257, -0.857730742533, -0.459757251779), (0.854444618044, -0.404156982541, 0.326468265163), (-0.465835971073, -0.317734333646, 0.825858184725)-70.1250151796, -50.0219972976, -61.0544653556
8given(0.0130572766948, 0.710025061258, -0.704055338671), (0.709635958224, -0.502634766144, -0.493735859199), (-0.704447524179, -0.493176139173, -0.510422355926)10.8788940267, -82.9477292019, -67.8280554759
9given(0.522722124832, -0.339909548335, 0.781807571697), (-0.343632695585, 0.755259014204, 0.558122201662), (-0.78017828138, -0.56039746646, 0.277986562354)-18.6568154521, 32.3334550403, -50.0497801427

-
Components

#1: Protein
U2 small nuclear ribonucleoprotein auxiliary factor-like protein


Mass: 26344.531 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MBM17.11, MBM17_11, At5g64010, AT5G64010 / Plasmid: pHAT4-atpaxx / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4KC77
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 20%(w/v) PEG550MME, 100 mM NaCl, 100 mM Bicine pH9.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9179 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 3.6→187.36 Å / Num. obs: 36248 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 95.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.242 / Net I/σ(I): 8
Reflection shellResolution: 3.6→3.76 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.401 / Mean I/σ(I) obs: 2 / Num. unique obs: 4339 / CC1/2: 0.889 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→152.42 Å / SU ML: 0.4866 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3505
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2859 1794 4.97 %
Rwork0.248 34268 -
obs0.2499 36062 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 119.85 Å2
Refinement stepCycle: LAST / Resolution: 3.6→152.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10120 0 0 22 10142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005810304
X-RAY DIFFRACTIONf_angle_d0.906514059
X-RAY DIFFRACTIONf_chiral_restr0.05851728
X-RAY DIFFRACTIONf_plane_restr0.00561773
X-RAY DIFFRACTIONf_dihedral_angle_d14.00593351
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.718854118234
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.902776500446
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.910361601182
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.699635839799
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.783374485421
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.759945367839
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.803344584698
ens_1d_9AX-RAY DIFFRACTIONTorsion NCS0.841074751752
ens_1d_10AX-RAY DIFFRACTIONTorsion NCS0.847733512475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.70.38071370.33442593X-RAY DIFFRACTION99.64
3.7-3.810.32861480.28482576X-RAY DIFFRACTION99.34
3.81-3.930.36891370.29982566X-RAY DIFFRACTION98.76
3.93-4.070.3621230.29632594X-RAY DIFFRACTION99.34
4.07-4.230.26111530.24182604X-RAY DIFFRACTION99.57
4.23-4.430.26131120.23842624X-RAY DIFFRACTION99.89
4.43-4.660.24241240.22642640X-RAY DIFFRACTION99.46
4.66-4.950.25711260.20722622X-RAY DIFFRACTION99.89
4.95-5.330.23871440.20562637X-RAY DIFFRACTION99.96
5.33-5.870.23721350.22522661X-RAY DIFFRACTION99.89
5.87-6.720.29331510.26962655X-RAY DIFFRACTION99.72
6.72-8.460.31381490.26632682X-RAY DIFFRACTION100
8.47-152.420.28921550.24022814X-RAY DIFFRACTION99.46
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)
12.11232935833-0.4474572277040.7486533941363.2811372639-0.9032435709040.877778816454-0.1096334551730.05792621870470.000388378859642-0.373640034487-0.406919584336-0.05182364845680.2915589780270.447553987132-0.0138847994630.7452117127540.217895026515-0.009481351191730.78856238290.01149738495330.625420526092-0.81238491056-55.6082688496-38.6418593858
24.06762751449-2.273763002151.551173955654.04499028748-0.6272588951373.98666188345-0.3488344741270.149998030479-1.58541229534E-5-0.0941775849025-0.1177239950830.01245495458650.094717695450.0014363248153-0.09712593120290.6851216975970.1870316730470.1342302076830.7349248334180.004089203081060.4388310898258.91393602171-74.5898574006-16.5924670792
33.68754939186-1.245625645580.7035311119851.3855537809-0.4642304529472.68082986481-0.1951591567890.362360920737-0.6311545513950.3100122277760.1011328346020.135759117315-0.403230140939-0.4107629351180.03698369239390.9003224681620.2893680011140.2008863939690.6802920259090.1084978403810.665752219761-47.5926635372.89497872563-17.5128657734
42.55354317887-0.666137858314-0.8115257455984.745675060811.909951081662.832716782660.521774925288-0.375508742873-0.006492538837-0.320247652589-0.268724623268-0.7619107458520.0341519607087-0.3454629511420.1852972228540.6287264370110.272510280660.202201464190.5640456615220.05508023250880.838534910056-22.5434839843-5.98282414819-33.8177245539
52.07977990731-0.512069902613-0.3428852149863.367541512551.900090529130.3292063809280.0157009379455-0.1564643567420.1371737976530.2595893208540.0904394682256-0.1687449283270.236038103491-0.1997513327060.03961496598410.726696655227-0.220530813817-0.1475234822380.8154518370770.1057427403620.92433055663-23.8436019211-72.8048989601-61.4335729414
61.379822144850.3500242593920.7335498583063.72467078124-2.008484296610.9480376061710.0768624043651-0.4461922333440.478478448573-0.1719665288860.1272242664360.1888205024910.112707697562-0.03210250933890.00259231037580.790800378743-0.168562946368-0.1135404167490.764311904577-0.02201745978330.88803138422-29.1350596603-42.9556012575-65.3728905069
75.021649971040.600707233016-0.5132100839185.622245927751.844961226272.59589244296-0.0151277233640.141559619204-0.3043337254160.332370952342-0.254783839216-0.006175753298470.04545732849160.05682947239537.28979307202E-50.727869994871-0.2187135790210.04450582167840.7079988978550.09095671810820.442726236308-0.557005036474-17.8019921041-55.2650933823
81.642708159912.85772782129-1.283699573252.854675432213.018991894393.1316156556-0.571060687423-0.117495790142-0.407969429280.04605183609860.697892941064-0.331465645103-0.516091694128-0.2226431866440.01598295659340.884663916714-0.3745080847230.1798054766910.715837683554-0.07832763202470.781634074612-4.83409982779-41.2958408366-74.6973222268
93.93253219065-0.6285288240960.07608620937761.34753945075-0.5870804996211.56508110542-0.1611468534580.1492826742970.798083567627-0.130270663390.0504690142783-0.560547499451-0.0819747338475-0.008322327224942.40729989095E-80.7190893444860.131172379405-0.1079787754470.643360769161-0.03589999966291.0375344889-1.14287383341-36.768455862-20.1904037921
101.88008032896-1.617964951092.768318013834.67300203850.6005286204982.618278876250.2082784664140.0614508432048-0.229414273748-0.2255977533150.0790747949270.275208187555-0.1637442569180.2224769455441.48505849973E-80.7021627245640.1768324859230.05248029501150.6486374428160.0395626424260.932710479798-29.9608991895-31.1503988278-30.4215183043
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 1 through 152)AA1 - 1521 - 140
22(chain 'B' and resid 1 through 152)BB1 - 1521 - 140
33(chain 'C' and resid 1 through 150)CC1 - 1501 - 137
44(chain 'D' and resid 1 through 151)DD1 - 1511 - 140
55(chain 'E' and resid 1 through 151)EE1 - 1511 - 137
66(chain 'F' and resid 1 through 155)FF1 - 1551 - 143
77(chain 'G' and resid 1 through 153)GG1 - 1531 - 143
88(chain 'H' and resid 1 through 150)HH1 - 1501 - 135
99(chain 'I' and resid 1 through 150)II1 - 1501 - 137
1010(chain 'J' and resid 1 through 150)JJ1 - 1501 - 147

+
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