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- PDB-7a1i: Crystal structure of the BILBO2/FPC4 complex -

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Basic information

Entry
Database: PDB / ID: 7a1i
TitleCrystal structure of the BILBO2/FPC4 complex
Components
  • BILBO1_N domain-containing protein
  • FPC4
KeywordsPEPTIDE BINDING PROTEIN / Complex / Cytoskeleton / Flagellum / Trypanosoma
Function / homologyBILBO1, N-terminal domain / BILBO1 N-terminal domain / HEXANE-1,6-DIOL / BILBO1_N domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesTrypanosoma brucei equiperdum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsDong, G.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP28231-B28 Austria
Austrian Science FundP24383-B21 Austria
CitationJournal: Plos Pathog. / Year: 2021
Title: Structural and functional studies of the first tripartite protein complex at the Trypanosoma brucei flagellar pocket collar.
Authors: Isch, C. / Majneri, P. / Landrein, N. / Pivovarova, Y. / Lesigang, J. / Lauruol, F. / Robinson, D.R. / Dong, G. / Bonhivers, M.
History
DepositionAug 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BILBO1_N domain-containing protein
B: FPC4
C: BILBO1_N domain-containing protein
D: FPC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,24311
Polymers36,6634
Non-polymers5807
Water1,47782
1
A: BILBO1_N domain-containing protein
B: FPC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5586
Polymers18,3322
Non-polymers2264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: BILBO1_N domain-containing protein
D: FPC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6855
Polymers18,3322
Non-polymers3533
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.418, 73.385, 120.514
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 12 or resid 14...
d_2ens_1(chain "C" and (resid 4 through 12 or resid 14...
d_1ens_2chain "B"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYASPA1 - 9
d_12ens_1ASPPHEA11 - 21
d_13ens_1GLYSERA25 - 29
d_14ens_1LEUPHEA31 - 43
d_15ens_1LEUASPA45 - 68
d_16ens_1LEUGLUA70 - 71
d_17ens_1THRGLYA73 - 102
d_18ens_1PROSERA104 - 107
d_21ens_1GLYASPG1 - 9
d_22ens_1ASPSERG13 - 28
d_23ens_1LEUPHEG30 - 42
d_24ens_1LEUASPG44 - 67
d_25ens_1LEUGLUG69 - 70
d_26ens_1THRGLYG72 - 101
d_27ens_1PROSERG103 - 106
d_11ens_2VALPROF1 - 7
d_21ens_2VALPROK1 - 7

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.131482831025, 0.991303880542, 0.00537415737243), (0.990556986982, 0.131592349283, -0.0384747859157), (-0.0388474025754, 0.000264635359133, -0.999245119719)29.1964543201, 6.52214852827, 31.3495311394
2given(-0.131115756828, 0.988062084981, 0.0808824735894), (0.988698904786, 0.136308731792, -0.0624051705557), (-0.0726851703321, 0.0717861118868, -0.994768123813)27.6164359204, 6.80293732047, 30.307264403

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein BILBO1_N domain-containing protein


Mass: 12466.060 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei equiperdum (eukaryote)
Gene: DPX39_060035600 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3L6L5Q1
#2: Protein FPC4


Mass: 5865.649 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei equiperdum (eukaryote)
Gene: DPX39_040053800 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3L6LBE5

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Non-polymers , 6 types, 89 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Details

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

CrystalDescription: diamond-like crystals with dimensions of approximately 100 x 50 x 50 micrometers
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 mM NaOAc (pH 4.5), 0.5 M 1,6-Hexanediol, and 10 mM CoCl2

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.87→46.64 Å / Num. obs: 21911 / % possible obs: 95.35 % / Redundancy: 12.4 % / Biso Wilson estimate: 39.39 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1247 / Rpim(I) all: 0.0369 / Rrim(I) all: 0.1302 / Net I/σ(I): 12.76
Reflection shellResolution: 1.87→1.937 Å / Redundancy: 9.7 % / Rmerge(I) obs: 2.359 / Mean I/σ(I) obs: 0.77 / Num. unique obs: 1295 / CC1/2: 0.742 / CC star: 0.923 / Rpim(I) all: 0.727 / Rrim(I) all: 2.477 / % possible all: 57.71

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PHENIX1.18_3845refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SJQ.pdb

6sjq


Resolution: 1.87→19.75 Å / SU ML: 0.2602 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.0256
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2507 1992 9.27 %
Rwork0.2119 19489 -
obs0.2156 21481 95.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.22 Å2
Refinement stepCycle: LAST / Resolution: 1.87→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 36 82 1880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661837
X-RAY DIFFRACTIONf_angle_d0.80962502
X-RAY DIFFRACTIONf_chiral_restr0.0559288
X-RAY DIFFRACTIONf_plane_restr0.0069320
X-RAY DIFFRACTIONf_dihedral_angle_d17.892664
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.894514357689
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.611152070452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.4625620.5179606X-RAY DIFFRACTION41.67
1.92-1.970.41571460.37051420X-RAY DIFFRACTION98.99
1.97-2.030.37441460.32271414X-RAY DIFFRACTION99.3
2.03-2.090.36031460.31951430X-RAY DIFFRACTION98.75
2.09-2.170.34511480.29931436X-RAY DIFFRACTION98.81
2.17-2.250.29791440.27481419X-RAY DIFFRACTION99.11
2.25-2.360.27591440.26481437X-RAY DIFFRACTION99.31
2.36-2.480.27881490.24181454X-RAY DIFFRACTION99.94
2.48-2.630.24151500.23131461X-RAY DIFFRACTION99.88
2.63-2.840.22311470.21931436X-RAY DIFFRACTION99.87
2.84-3.120.27961480.21051456X-RAY DIFFRACTION99.69
3.12-3.570.22961510.18751473X-RAY DIFFRACTION99.57
3.57-4.490.2191520.17061486X-RAY DIFFRACTION100
4.49-19.750.22651590.18651561X-RAY DIFFRACTION99.77
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)
14.614658263820.598579105533-0.4586733646013.792911630870.01130045656596.93050364506-0.2917470408350.3334659324260.0289746990486-0.2816682785510.15819311754-0.06969667331990.272975167778-0.2375865758840.1944069348780.435381128038-0.00971076227523-0.07514854214190.353395432285-0.05038318232740.35896785195916.80282941710.739662052623.7579815508
24.20626857536-0.4466478728391.275226816216.003615906792.178573233594.20313740626-0.253421503265-0.0907848443067-0.3073409220290.316635405620.1312838719240.2384992366190.662783614499-0.05926777039170.04407380656160.437844613803-0.0491292664033-0.0274014587040.281689712191-0.00151251753710.32471414502324.44011021216.878088005325.9690671788
38.50498387592-3.0369110602-4.454128032563.409443131111.502356365299.49165534761-0.420639623688-1.049393486710.8069586188110.2509632505690.05547474145890.319996145569-0.872971723341-0.788482575242-0.1624802474350.684920351559-0.0382034514928-0.03802657040570.476679858077-0.09756462399330.53044796453716.663694810224.731219521229.8527385497
46.18059604285-6.386587168740.4678653600146.683275238-0.6079570273722.41980956249-0.14404866408-0.9115808319230.379302762404-0.2693734052010.3041422323820.0199455764744-1.1599304880.573983876421-0.3057338680220.507500454382-0.07574520359760.02206496104540.556567048909-0.07484888875370.3718434836420.492305631319.201474639138.6222881576
54.00419889039-1.718012636332.359243638492.693172168980.6276448166332.66866542217-0.0461967745160.2746233055980.864058149984-0.1987858925610.01367861638390.4011407522170.00990825662846-0.5093541935820.09634759305860.432160389517-0.041452840523-0.04714181405450.2369755343390.02088661308730.42569055127521.091520031817.69554556223.5804189568
65.18388998119-0.6334434962860.8817035062597.16247178352-1.579701193593.820038577590.1961094002780.108619899219-0.9534506969030.1136532004640.001788845468150.9539379885350.8076446411970.00659229326218-0.1157249404160.620685533063-0.03936468704340.05423758570250.444596218363-0.002623943439790.3866895974715.1103352815.2902641835522.3366190528
72.823867944091.805065937722.647803058232.377557844491.330606051169.25335895535-0.259993131527-0.8309798099631.80766534643-0.5892191451540.1099241925480.015362320901-0.7262066604041.165881287870.1555611412940.44789438447-0.0718795070718-0.05677083186810.443917068366-0.05778954257890.45786104960617.91068699723.466100484120.476900297
84.89217212391-0.336139466217-0.3952591346895.57577306963-0.8565315924176.74451482887-0.05091886365470.327168389926-0.124951598375-0.393073199475-0.2351890728520.09893418640990.173866483619-0.7080026529980.3071421533560.540123463039-0.01185397974540.03627871966950.3835524871370.01625247269940.34371216764737.43455560723.69822707015.50696902691
95.22170263007-0.25193263227-3.007885041924.3044407295-0.311763349019.04170444869-0.3149582653230.530908528097-0.218071698277-0.335989421807-0.1900341550620.3046806806580.50335072652-1.035897296340.4976110486890.393685384784-0.06793782283920.007252386678650.4338243794340.008078482105740.34795315057531.637435314730.24673979174.40379052817
107.317606180022.78207257577-5.144507333012.5051287136-1.64768660728.054228382120.585201683492-0.7663970960350.2778417019370.78899538459-0.579983400942-0.218141916782-0.4038988083630.1556687224080.1784213402870.523524834686-0.0339278073750.006795552793350.398090787130.03577004099970.46165556692234.379926518536.574261836311.2608496011
113.77993597688-0.417286697255-0.4656657953753.186171303591.99730813285.476487656760.03881193286420.1136278223930.170386535836-0.0737628628335-0.00922573160002-0.9751194195770.320174259771.58521214119-0.3766317229320.729018399320.1083072570410.06748705925590.6642665774010.05869890248580.57072691224550.080507905226.0403020253-1.87702308472
122.593325994750.17300496781-0.8732097957553.34428548104-4.162790542635.21190910559-0.0845911985006-0.0686486691432-0.219525055119-0.108167041792-0.224834512298-0.2011673170570.1838116836780.2018103890370.1917757964060.3080365045740.00488839430239-0.03275649644680.332150259480.1063917146670.37785613963644.143542797328.57614052947.21552434169
135.425413506835.851629307053.556540054667.070330096072.970335381146.211962382450.509836291057-0.127758235248-0.535487947686-0.0635740142765-0.0994131772988-0.1780568975081.29843720786-0.864480433856-0.09226465094710.562788330573-0.0824232586469-0.03747657379520.3866060512030.1003225693220.39187868722839.08236459319.264436523311.8552859407
142.84458156683-2.854202440020.9540580801433.86909828569-1.872081107011.428929931461.33287715658-0.23835883649-1.48477870232-1.853344312650.2322905662831.687816269861.41079539965-1.46855521478-0.8394151821720.926513793988-0.0919046728863-0.07066133692040.6332900337730.09904467512760.63880935101827.063368911123.04696315035.5832813937
157.85677753981-0.598477344958-0.208273314275.03360370352-3.436219700443.69490832908-0.159677174893-0.02505176348180.5423241555350.363319968176-1.05398124897-1.3548732945-0.5019778874751.063338163261.077403891950.6833706040460.0201785527155-0.09648718470860.530344649280.1361419042330.5423906934750.115927159926.415915234110.3324672834
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 24 )AA4 - 241 - 21
22chain 'A' and (resid 25 through 58 )AA25 - 5822 - 55
33chain 'A' and (resid 59 through 72 )AA59 - 7256 - 69
44chain 'A' and (resid 73 through 78 )AA73 - 7870 - 75
55chain 'A' and (resid 79 through 98 )AA79 - 9876 - 95
66chain 'A' and (resid 99 through 110 )AA99 - 11096 - 107
77chain 'B' and (resid 432 through 438 )BF432 - 4381 - 7
88chain 'C' and (resid 4 through 30 )CG4 - 301 - 26
99chain 'C' and (resid 31 through 48 )CG31 - 4827 - 44
1010chain 'C' and (resid 49 through 58 )CG49 - 5845 - 54
1111chain 'C' and (resid 59 through 78 )CG59 - 7855 - 74
1212chain 'C' and (resid 79 through 98 )CG79 - 9875 - 94
1313chain 'C' and (resid 99 through 103 )CG99 - 10395 - 99
1414chain 'C' and (resid 104 through 110 )CG104 - 110100 - 106
1515chain 'D' and (resid 432 through 438 )DK432 - 4381 - 7

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