[English] 日本語
Yorodumi
- PDB-6s9y: Crystal structure of the N-terminal domain of the wild type paras... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s9y
TitleCrystal structure of the N-terminal domain of the wild type parasitic PEX14
ComponentsPeroxin 14
KeywordsSIGNALING PROTEIN / PEX14 / PPI / PEX14/PEX5 / Trypanosomes / FBDD
Function / homology
Function and homology information


glycosome membrane / protein import into peroxisome matrix, docking / protein targeting to vacuole / glycosome / post-transcriptional regulation of gene expression
Similarity search - Function
Peroxisome membrane anchor protein Pex14p, N-terminal / Peroxisomal membrane protein 14 / Pex14 N-terminal domain / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Peroxisomal membrane protein PEX14
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsHassaan, E. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Commission Germany
CitationJournal: To Be Published
Title: Crystallographic Fragment Screening of the parasitic PEX14
Authors: Hassaan, E. / Heine, A. / Klebe, G.
History
DepositionJul 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxin 14
B: Peroxin 14
C: Peroxin 14
D: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4796
Polymers30,2674
Non-polymers2122
Water1,58588
1
A: Peroxin 14


Theoretical massNumber of molelcules
Total (without water)7,5671
Polymers7,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxin 14


Theoretical massNumber of molelcules
Total (without water)7,5671
Polymers7,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6732
Polymers7,5671
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6732
Polymers7,5671
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.925, 81.268, 39.287
Angle α, β, γ (deg.)90.000, 92.750, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 5 or (resid 6 and (name...A5
121(chain 'A' and (resid 5 or (resid 6 and (name...A8 - 20
131(chain 'A' and (resid 5 or (resid 6 and (name...A22 - 58
141(chain 'A' and (resid 5 or (resid 6 and (name...A61 - 66
251(chain 'B' and (resid 5 or (resid 6 and (name...B5
261(chain 'B' and (resid 5 or (resid 6 and (name...B8 - 20
271(chain 'B' and (resid 5 or (resid 6 and (name...B22 - 58
281(chain 'B' and (resid 5 or (resid 6 and (name...B61 - 66
391(chain 'C' and (resid 5 or (resid 6 and (name...C5
3101(chain 'C' and (resid 5 or (resid 6 and (name...C8 - 20
3111(chain 'C' and (resid 5 or (resid 6 and (name...C22 - 58
3121(chain 'C' and (resid 5 or (resid 6 and (name...C61 - 66
4131(chain 'D' and (resid 5 through 6 or resid 8...D5
4141(chain 'D' and (resid 5 through 6 or resid 8...D8 - 20
4151(chain 'D' and (resid 5 through 6 or resid 8...D22 - 58
4161(chain 'D' and (resid 5 through 6 or resid 8...D61 - 66

-
Components

#1: Protein
Peroxin 14 /


Mass: 7566.653 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PEX14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IEW2
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.10 M trisodium citrate pH 5.5, 40% PEG 600

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.64→40.63 Å / Num. obs: 28782 / % possible obs: 96.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.63 Å2 / CC1/2: 0.998 / Rsym value: 0.061 / Net I/σ(I): 12.4
Reflection shellResolution: 1.64→1.74 Å / Num. unique obs: 3967 / CC1/2: 0.862 / Rsym value: 0.374

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHASERphasing
Cootmodel building
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→39.24 Å / SU ML: 0.1792 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.3073
RfactorNum. reflection% reflection
Rfree0.2291 1438 5 %
Rwork0.1971 --
obs0.1986 28758 96.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.03 Å2
Refinement stepCycle: LAST / Resolution: 1.64→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 14 88 1968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511925
X-RAY DIFFRACTIONf_angle_d0.70362588
X-RAY DIFFRACTIONf_chiral_restr0.0415317
X-RAY DIFFRACTIONf_plane_restr0.0053324
X-RAY DIFFRACTIONf_dihedral_angle_d17.37321210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.64-1.70.2821116220178.2
1.7-1.770.25391380.2248264792.99
1.77-1.850.27961470.2165279399.59
1.85-1.940.26141490.2013283598.71
1.94-2.070.23961470.1884278898.79
2.07-2.230.21981470.1793278599.15
2.23-2.450.21861490.1848283698.48
2.45-2.80.23141480.2014280498.8
2.8-3.530.23021470.2037279598.49
3.530.20651500.192283698.19
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)
10.06549185258630.0475547838292-0.07066075303530.0522735197164-0.04037332250540.05985508685960.07393711316510.0428747500730.00325083088175-0.219671516035-0.0432334772571-0.0504082019974-0.116306796176-0.1266118810947.72274588779E-50.2091751653590.00335304124725-0.02942013256350.1422518407850.01159806017950.15351017926519.33546590660.5489247208-41.5430849761
20.00828003328674-0.00512413521579-0.00662251323510.00633549720393-0.003807363460080.0100733175823-0.004377813432020.00561289700882-0.07334128502130.1021913332460.0898671650526-0.1047954602780.01604929662960.0305580972790.0002882605721480.19307834253-0.06050733499160.06834755616260.271167442873-0.08778036168180.32237772840225.674923257865.6061308477-35.4350677517
30.2045491910060.0765036188018-0.1269699260460.0314480186915-0.03335697861910.160781585338-0.0100312581423-0.04867358449190.092655507491-0.07917788253610.0898247777325-0.0510588346430.01650944782670.1531694207670.09869838828780.2213510492940.03939448083390.2394604654750.230640936363-0.01157095321130.36242935488328.09864155960.9948100971-46.6722972141
40.0596636449668-0.0724727476975-0.0381636995640.1825020376660.03937743902370.0241659943996-0.0942234588952-0.0550317962099-0.09504318199070.374106916506-0.02083707735480.1742751955920.236515526747-0.12877056421-0.09423341255290.617899001882-0.02424449786090.5136904758240.137721804641-0.2043170441940.355590923736-4.5209172887562.811433227-13.7136517505
50.2605782362520.0911988148849-0.1292153297020.2749853261790.1032952351520.102821435569-0.05430009541330.0731475451688-0.03340820780630.522517530188-0.01498922592220.2010509487860.0683654693093-0.0148706057831-0.01105670548130.2191298323320.0043731749201-0.01631732672210.121567943237-0.008294879749380.1915004297610.61956011055264.9149578541-19.1689859855
60.0419011422441-0.0103047376132-0.00319986889070.009108101837860.003708984949080.002956951760180.02809128823030.05803247639940.0342492626891-0.1175000238440.03871730869960.108793046848-0.0979169119031-0.04152342446980.0003266312671710.212495855751-0.03629417137520.01644453977250.269367377538-0.02675047599340.3084257688750.12158917352958.1090482983-26.1535327588
70.01321267577230.00119013491909-0.01755043554970.0149884733855-0.007869009767120.02034093592860.0266132432850.07711821172630.0598012525376-0.01595294472310.0274572711499-0.0440300199271-0.02632497945640.03515335087010.01476590460140.2118670105450.02889804765830.07303320064460.2309478359440.02936702972380.25426877863310.210036610862.5919148188-26.0334902284
80.09409994917320.06244165722740.0004043489090450.1700328057760.01492819880740.015523931595-0.139840452153-0.002554036769040.1332708163430.1308779639460.0007538834764080.0376818023505-0.02302444320760.207706987919-0.01297295140750.1338799298050.0104707486827-0.01265080831810.137791448370.006191260246290.09168688107259.7402082704780.5347185728-18.3466370225
90.01319244141165.78535701231E-50.0007840568092490.0047676561132-0.009823148648760.006841627129190.00239625725098-0.1649351925020.08911229457880.1324782753190.14380294921-0.0084088110058-0.0660507195354-0.05144458140413.06527042955E-50.1835088469080.0397430698569-0.01404383505950.199179736502-0.01986149488140.1628313221460.01925911057791.0887746957-11.4380730325
100.01180165061620.008571663587540.01925011150240.01070559649360.01615805730890.02003646688330.0611644276401-0.00270854520510.329458962787-0.08457862597090.00866624260978-0.123843664851-0.137877931780.0500671890959-0.0001596798898130.179167354252-0.00524257187182-0.04781184310630.1237416810470.00502445976350.1601771547441.3135724834488.9084046971-22.9664025135
110.001735083112940.01344485437030.0006956582571210.0141677592801-0.008239033332470.002118938028490.06470276404490.133492871753-0.0736019573472-0.164984588175-0.0818919412780.08113876031650.0870693363001-0.005155640775275.60200040927E-50.1207004571150.0106781995245-0.008729237739690.134733490676-0.008450253176320.1187359834333.6549123661679.4977360458-22.4644985544
120.0119572412225-0.0004933598693260.0205501385960.003913501095870.003572330891780.02926109742420.003111130684540.1068290074750.009247245304-0.03514083448020.05669729309290.1896899226860.0586767254131-0.06399710405986.75700424659E-50.12984589673-0.0021137715048-0.01593783771050.1761871928610.007293989934850.19398977137-4.1530633730378.4104355329-17.5122582553
130.0104305486865-0.0192434759985-0.0004024886931850.05724478848160.03574280626020.029864071186-0.00438833110094-0.08785728956630.07051731913620.0597632665286-0.1285422497740.03866505614160.02805678876460.052750989538-0.02797461050770.1102777832040.0141555130828-0.06012271926630.188321687124-0.01041728094650.182957614357-5.9237442675982.8021753437-28.0228726656
140.1386583576290.1125418737160.02523382121340.09329796760810.0575258008430.03228855755010.12313652657-0.02992914126090.03342844306460.173113415648-0.0435856315416-0.1647879718080.165139731577-0.00950891263012-0.0005771213780590.1224665601490.0130867260219-0.02022779946680.15874744267-0.02078296668960.16018741649424.110352793280.6867796186-32.6380975871
150.00625185348355-0.008472782809460.006830424251130.0111060017121-0.008584676294720.00314973361242-0.01960590666730.03838465841990.0205682365465-0.273730113528-0.00902630623887-0.0194881200770.202057165881-0.0837725061945-0.0002605104805220.151991882895-0.00333448092001-0.03845986004460.1266653010970.003427260126810.15942590711617.514028832475.4317426758-38.4412249397
160.01797094786240.01483904043530.06882114670990.005435248398740.02811867218180.243399390015-0.1224148999670.02166040973610.163630029770.0108055344190.1029202934470.145072905881-0.312828269277-0.174979759335-0.004709308916270.1285763971750.014565796838-0.006808169495440.132261097462-0.004442779084270.12380769164218.447077037684.7728247338-36.4353692221
170.0093391173775-0.001335193979710.0105924537560.004985609023120.0009903229191940.007322735848170.01049119672230.07188265595090.0910107315732-0.0994990986358-0.03085133807030.1890744235170.0785836448416-0.132644077479-2.22859120021E-60.172672909337-0.0250963889165-0.03431420528380.2011378009120.02680756653250.1616259338223.327516593785.8660866243-44.0053817238
180.00896782087189-0.00703613740690.009751744300150.003980680571210.0008396624105280.02816590560890.05873701767330.02743603704880.06095447386550.02091853463050.03303235416960.0730481181308-0.0182345600590.109171612120.0002591073649040.143695078901-0.00097469743889-0.04273968929660.137564055821-0.0019769195610.12675946192312.350323881381.5241334256-45.91027199
190.01537141673470.0257553731895-0.01446843791160.09962135312280.08926407089870.1003588764810.0198723538087-0.0008512211789970.06157983216110.1763413108330.002442835801920.182911783444-0.0121828470769-0.01219100813-0.0001178124181130.2334788161750.01209504613190.03069526214180.164060587320.01682160651440.20807622365114.856064645760.3050131074-35.7239452345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 28 through 51 )
2X-RAY DIFFRACTION2chain 'C' and (resid 52 through 57 )
3X-RAY DIFFRACTION3chain 'C' and (resid 58 through 66 )
4X-RAY DIFFRACTION4chain 'D' and (resid 9 through 19 )
5X-RAY DIFFRACTION5chain 'D' and (resid 20 through 52 )
6X-RAY DIFFRACTION6chain 'D' and (resid 53 through 57 )
7X-RAY DIFFRACTION7chain 'D' and (resid 58 through 66 )
8X-RAY DIFFRACTION8chain 'A' and (resid 5 through 19 )
9X-RAY DIFFRACTION9chain 'A' and (resid 20 through 27 )
10X-RAY DIFFRACTION10chain 'A' and (resid 28 through 37 )
11X-RAY DIFFRACTION11chain 'A' and (resid 38 through 51 )
12X-RAY DIFFRACTION12chain 'A' and (resid 52 through 57 )
13X-RAY DIFFRACTION13chain 'A' and (resid 58 through 66 )
14X-RAY DIFFRACTION14chain 'B' and (resid 4 through 27 )
15X-RAY DIFFRACTION15chain 'B' and (resid 28 through 37 )
16X-RAY DIFFRACTION16chain 'B' and (resid 38 through 51 )
17X-RAY DIFFRACTION17chain 'B' and (resid 52 through 57 )
18X-RAY DIFFRACTION18chain 'B' and (resid 58 through 66 )
19X-RAY DIFFRACTION19chain 'C' and (resid 5 through 27 )

+
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