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- PDB-8q2d: Crystal structure of the E. coli PqiC Lipoprotein residues 17-187 -

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Basic information

Entry
Database: PDB / ID: 8q2d
TitleCrystal structure of the E. coli PqiC Lipoprotein residues 17-187
ComponentsIntermembrane transport lipoprotein PqiC
KeywordsTRANSPORT PROTEIN / Outermembrane lipoprotein
Function / homology: / ABC-type transport auxiliary lipoprotein component / ABC-type transport auxiliary lipoprotein component / membrane organization / cell outer membrane / outer membrane-bounded periplasmic space / Prokaryotic membrane lipoprotein lipid attachment site profile. / identical protein binding / Intermembrane transport lipoprotein PqiC
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsCooper, B.F. / Knowles, T.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M01116X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S017283/1 United Kingdom
CitationJournal: Embo Rep. / Year: 2024
Title: An octameric PqiC toroid stabilises the outer-membrane interaction of the PqiABC transport system.
Authors: Cooper, B.F. / Ratkeviciute, G. / Clifton, L.A. / Johnston, H. / Holyfield, R. / Hardy, D.J. / Caulton, S.G. / Chatterton, W. / Sridhar, P. / Wotherspoon, P. / Hughes, G.W. / Hall, S.C. / ...Authors: Cooper, B.F. / Ratkeviciute, G. / Clifton, L.A. / Johnston, H. / Holyfield, R. / Hardy, D.J. / Caulton, S.G. / Chatterton, W. / Sridhar, P. / Wotherspoon, P. / Hughes, G.W. / Hall, S.C. / Lovering, A.L. / Knowles, T.J.
History
DepositionAug 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Intermembrane transport lipoprotein PqiC
B: Intermembrane transport lipoprotein PqiC
C: Intermembrane transport lipoprotein PqiC


Theoretical massNumber of molelcules
Total (without water)57,3613
Polymers57,3613
Non-polymers00
Water5,675315
1
A: Intermembrane transport lipoprotein PqiC


  • defined by author
  • Evidence: gel filtration
  • 19.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)19,1201
Polymers19,1201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Intermembrane transport lipoprotein PqiC


  • defined by author
  • 19.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)19,1201
Polymers19,1201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Intermembrane transport lipoprotein PqiC


  • defined by author
  • 19.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)19,1201
Polymers19,1201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.603, 133.603, 65.715
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 22 through 187)
d_3ens_1(chain "C" and resid 22 through 187)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 22 - 187 / Label seq-ID: 8 - 173

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC

NCS oper:
IDCodeMatrixVector
1given(0.492723231208, 0.866200813077, -0.0831863501622), (-0.85831046013, 0.499512630595, 0.117432048044), (0.143272368096, 0.0135382163246, 0.989590695813)66.6291157336, 38.6466420637, -17.7833478224
2given(-0.87449395915, 0.46416002707, 0.140768550042), (-0.461838619495, -0.885510997944, 0.0507480252106), (0.148207303982, -0.0206335113343, 0.98874104459)77.0273478884, -5.13950550339, 17.7515449257

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Components

#1: Protein Intermembrane transport lipoprotein PqiC


Mass: 19120.336 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pqiC, ymbA, b0952, JW5127 / Production host: Escherichia coli (E. coli) / Variant (production host): C43 / References: UniProt: P0AB10
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M sodium chloride, 0.1 M MES; pH 6.5, 33% v/v PEG 400, 4% v/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→43.73 Å / Num. obs: 67192 / % possible obs: 84 % / Redundancy: 2 % / Biso Wilson estimate: 46.75 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.79
Reflection shellResolution: 2.08→2.15 Å / Num. unique obs: 450 / CC1/2: 0.613

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→43.73 Å / SU ML: 0.2698 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.5452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2293 1683 4.97 %
Rwork0.2037 32165 -
obs0.2049 33848 83.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.89 Å2
Refinement stepCycle: LAST / Resolution: 2.08→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3640 0 0 315 3955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493715
X-RAY DIFFRACTIONf_angle_d0.80025080
X-RAY DIFFRACTIONf_chiral_restr0.053583
X-RAY DIFFRACTIONf_plane_restr0.007656
X-RAY DIFFRACTIONf_dihedral_angle_d14.38491335
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.976124948477
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.77489270526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.140.39650.3444156X-RAY DIFFRACTION4.86
2.14-2.210.3656370.3039533X-RAY DIFFRACTION17.28
2.21-2.290.32371580.30752632X-RAY DIFFRACTION82.59
2.29-2.380.30211730.26533160X-RAY DIFFRACTION99.97
2.38-2.490.26121690.25833167X-RAY DIFFRACTION100
2.49-2.620.28341530.25533222X-RAY DIFFRACTION100
2.62-2.780.30961810.24963151X-RAY DIFFRACTION100
2.78-30.30241850.24573177X-RAY DIFFRACTION100
3-3.30.26511570.22813211X-RAY DIFFRACTION100
3.3-3.780.23331540.19143216X-RAY DIFFRACTION99.97
3.78-4.760.16721600.16073234X-RAY DIFFRACTION100
4.76-43.730.18191510.17783306X-RAY DIFFRACTION99.83
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)
11.848749503741.4876739022-1.846286205965.351876562612.483820905385.837885191690.230812319475-0.1440211727960.352964338614-0.06364976288910.156996683801-0.170898691055-0.1400540353470.422760764984-0.3536439871560.2443562903950.0381537905830.01886569950640.398600995360.02419454117680.43958498959253.3152052423-18.7290456444.58393408595
21.12099279956-0.263973796107-0.5447269234923.581307953632.377704268513.977988869150.1125186297640.02872875326470.187608133041-0.1449349763010.13164531204-0.0821894012722-0.1753974609820.0244034691042-0.2567341462450.3169089624660.0452396393720.01943728157450.3652383102020.08074479913710.39642944790947.9622460393-22.1876489997.61552466148
32.554980901880.8784418133420.2216930183683.036617480041.886483502095.398895219230.2072012553310.1417635478990.168267080519-0.0243791613893-0.1013000280940.1815586387860.217530416046-0.6989955386810.08879804185810.3491333205430.1208647140450.05072071552870.4758837424520.09451883282450.47013900724939.0006238131-21.5757909229.03592634102
41.81485498297-1.18137196593-1.257120483844.293788779833.370774529225.638499106590.4757434123870.4138578822690.31855142783-0.198905342294-0.2631654966750.167086366222-0.484502185768-0.943332437963-0.0108460561780.3901616442120.08505648052210.05472803619490.424777168010.09613785922730.46175335218940.7799101939-16.19845817116.03837177686
56.26292694461-1.75442843611.646459622867.25348756109-0.1680479886791.960123876430.2618226721380.606216106144-1.39494572963-0.4198576888940.07125943931640.3895676022970.402549150435-0.989929125847-0.4422132834370.455716173235-0.02480496611440.01031482585330.593487353645-0.06320871536130.58734534180871.9125802089-24.894927139-20.3046367739
62.654067660950.7941737606290.510415562352.54681505423-0.09210294295350.843956645342-0.0274040603582-0.392956503476-0.00190731276810.4667905771530.0963198291067-0.492213326791-0.8734845485750.863260688523-0.002005126175280.769450329654-0.2393751654370.02245598618650.601456178764-0.1208789611720.54105716169277.8354921574-12.1268267767-0.217190227533
74.903999646093.042590583920.9392775805361.91337960276-0.01382642361596.609730133790.04617377937560.266999932079-0.0544140026047-0.1505424509510.148351596183-0.148365737121-0.426286678745-0.272424734782-0.1655425178920.45888217980.01640144444590.02924204097960.4000100549910.0577834068420.47960909957860.5405383381-20.8363252889-10.0064530016
82.89309004560.06510176161950.645695472872.70265964145-0.7851949932353.27867363714-0.0854146513084-0.01550075041510.08062893627080.2322922194240.0896060607649-0.419655048649-0.756954841370.5622152676290.06419206943770.55085552779-0.133725317120.009734168347950.425254536072-0.01182254985210.48344873057776.6700515998-13.8186491752-5.90317236916
92.270281763790.331055365416-0.3827281525624.20360494355-0.06310936996042.822785820310.116679373962-0.255060019350.4840140528180.7481801806910.0138736606442-0.113068039339-1.399558097480.792657092776-0.07272350747420.905356159335-0.2339344291630.152703876480.515069862405-0.03442518803110.47418918416472.4507009094-7.724076987071.0255406108
103.534953629420.6089785594521.828002245392.890811910730.2586511104111.914642827590.386771973619-0.392610737520.8484638019390.938720032783-0.6524761099050.799244664939-0.3214074960390.08315712372550.2122993026641.24318261925-0.03610048663680.184230330950.452548413552-0.101287231450.55885498051366.8619288863-2.782309712832.98998344118
112.747078038781.171607400572.754395246782.11134134879-0.1730187076623.8859800758-0.7336740518571.38863038526-0.049034361329-0.7758189497070.02740377254110.166039706467-1.0710997130.318475154370.444577896710.970233192847-0.078581734856-0.04626435324960.544601277501-0.008096506062460.44909149959864.3854537286-10.3832053156-23.0796734237
123.227113049661.215612624171.023343242593.814453644732.562115869742.389383749550.415257662298-0.03732340913640.7651471691250.424575341026-0.4675583522170.130512391736-1.53554421194-0.0725053454399-0.0001701399043021.24381561424-0.2324906062980.2202335177350.3062506007160.02090766868460.48245660460772.2233415186-3.77974615583-6.30987803886
134.69523158953-0.3230615223115.24619982151.535561396260.2642740267039.837278172590.2644720838270.983958750958-0.6056078422280.084014437893-0.3029628005780.0700573932112-0.04937918251551.054695865810.04098087054010.27500066899-0.0318996246158-0.01507798869780.3815440022990.01868090997440.42360003709519.091888538-11.712678062121.8557294757
143.36925330547-1.16796287130.2336358315493.0546574362-0.3962643975292.685281732260.0328707557272-0.428387347244-0.3607103782030.1501272801470.06337769167980.2093410226640.234577809348-0.0812143582333-0.08675139232150.317549911789-0.01009735630440.01364087075880.3445401139520.01171086574310.31989417798924.1449267439-9.6605783082433.1293938684
153.22690501210.0935449200346-0.7071683921625.83168627581-2.125661969473.951180933440.0722214753445-0.3638649139920.2508099316560.399476156743-0.0477301559438-0.346589542306-0.2738797401560.3131793382480.03282723577540.352857124105-0.0218199459140.03289183159680.353915425728-0.05583083636010.36020657624731.6607078158-3.5895767275234.1098411186
164.40245651593-0.5705028633561.637066464084.03557379462-2.427442818515.13658128718-0.355694546827-0.01220765367610.1293952476250.070732006071-0.0445193435137-0.53469859397-0.03457524356140.5332589243720.2697662285790.4269165284670.04222487456450.04162895976850.399676190724-0.004663941714450.41286509140934.5928680279-9.2703168220929.9676316288
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 22 through 53 )AA22 - 531 - 19
22chain 'A' and (resid 54 through 141 )AA54 - 14120 - 107
33chain 'A' and (resid 142 through 160 )AA142 - 160108 - 126
44chain 'A' and (resid 161 through 187 )AA161 - 187127 - 153
55chain 'B' and (resid 21 through 26 )BB21 - 261 - 6
66chain 'B' and (resid 27 through 53 )BB27 - 537 - 20
77chain 'B' and (resid 54 through 76 )BB54 - 7621 - 43
88chain 'B' and (resid 77 through 98 )BB77 - 9844 - 65
99chain 'B' and (resid 99 through 141 )BB99 - 14166 - 108
1010chain 'B' and (resid 142 through 155 )BB142 - 155109 - 122
1111chain 'B' and (resid 156 through 160 )BB156 - 160123 - 127
1212chain 'B' and (resid 161 through 187 )BB161 - 187128 - 154
1313chain 'C' and (resid 21 through 45 )CC21 - 451 - 12
1414chain 'C' and (resid 46 through 113 )CC46 - 11313 - 80
1515chain 'C' and (resid 114 through 160 )CC114 - 16081 - 127
1616chain 'C' and (resid 161 through 187 )CC161 - 187128 - 154

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