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- PDB-6s9y: Crystal structure of the N-terminal domain of the wild type paras... -

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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 / peroxisomal importomer complex / protein import into peroxisome matrix, docking / protein targeting to vacuole / glycosome / post-transcriptional regulation of gene expression / signaling receptor binding
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
Revision 1.1May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSER(chain 'A' and (resid 5 or (resid 6 and (name...AA55
12GLUGLUASPASP(chain 'A' and (resid 5 or (resid 6 and (name...AA8 - 208 - 20
13ARGARGLEULEU(chain 'A' and (resid 5 or (resid 6 and (name...AA22 - 5822 - 58
14ILEILESERSER(chain 'A' and (resid 5 or (resid 6 and (name...AA61 - 6661 - 66
25SERSERSERSER(chain 'B' and (resid 5 or (resid 6 and (name...BB55
26GLUGLUASPASP(chain 'B' and (resid 5 or (resid 6 and (name...BB8 - 208 - 20
27ARGARGLEULEU(chain 'B' and (resid 5 or (resid 6 and (name...BB22 - 5822 - 58
28ILEILESERSER(chain 'B' and (resid 5 or (resid 6 and (name...BB61 - 6661 - 66
39SERSERSERSER(chain 'C' and (resid 5 or (resid 6 and (name...CC55
310GLUGLUASPASP(chain 'C' and (resid 5 or (resid 6 and (name...CC8 - 208 - 20
311ARGARGLEULEU(chain 'C' and (resid 5 or (resid 6 and (name...CC22 - 5822 - 58
312ILEILESERSER(chain 'C' and (resid 5 or (resid 6 and (name...CC61 - 6661 - 66
413SERSERSERSER(chain 'D' and (resid 5 through 6 or resid 8...DD55
414GLUGLUASPASP(chain 'D' and (resid 5 through 6 or resid 8...DD8 - 208 - 20
415ARGARGLEULEU(chain 'D' and (resid 5 through 6 or resid 8...DD22 - 5822 - 58
416ILEILESERSER(chain 'D' and (resid 5 through 6 or resid 8...DD61 - 6661 - 66

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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


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


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

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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: 2.18 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

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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

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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 )

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