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- PDB-9fzd: Structure of OmpA-long in complex with nanobody Nb39 -

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Basic information

Entry
Database: PDB / ID: 9fzd
TitleStructure of OmpA-long in complex with nanobody Nb39
Components
  • Nanobody 39
  • Outer membrane protein A
KeywordsMEMBRANE PROTEIN / Porin / Nanobody / Complex
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family ...Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Outer membrane protein/outer membrane enzyme PagP, beta-barrel
Similarity search - Domain/homology
Outer membrane protein A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAckle, F. / Sorgenfrei, M. / Seeger, M.A.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation407240_177368 Switzerland
Swiss National Science FoundationPP00P3_170625 Switzerland
CitationJournal: To Be Published
Title: Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies
Authors: Sorgenfrei, M. / Hurlimann, L.M. / Printz, A. / Wegner, F. / Morger, D. / Ackle, F. / Remy, M.M. / Montowski, G. / Keserue, H. / Cuenod, A. / Imkamp, F. / Egli, A. / Keller, P.M. / Seeger, M.A.
History
DepositionJul 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein A
B: Nanobody 39


Theoretical massNumber of molelcules
Total (without water)32,4742
Polymers32,4742
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Pull-down
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-6 kcal/mol
Surface area13960 Å2
Unit cell
Length a, b, c (Å)52.398, 52.572, 256.746
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Outer membrane protein A / Outer membrane porin A


Mass: 19284.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Clinical isolate / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ompA, c1093 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): MC1061 / References: UniProt: A0A0H2V5V4
#2: Antibody Nanobody 39 / Nb39


Mass: 13189.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): MC1061
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium chloride, 0.1 M sodium citrate, 12 % PEG 4K, 0.1 M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→44.8 Å / Num. obs: 16264 / % possible obs: 99.57 % / Redundancy: 13.2 % / Biso Wilson estimate: 56.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07108 / Rpim(I) all: 0.02042 / Rrim(I) all: 0.07406 / Net I/σ(I): 22.03
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 3.17 / Num. unique obs: 1601 / CC1/2: 0.879 / Rpim(I) all: 0.2518 / Rrim(I) all: 0.9333 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.8 Å / SU ML: 0.3213 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2579
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2829 814 5.01 %
Rwork0.2556 15437 -
obs0.2569 16251 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 0 16 2271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01292314
X-RAY DIFFRACTIONf_angle_d1.79743147
X-RAY DIFFRACTIONf_chiral_restr0.1002328
X-RAY DIFFRACTIONf_plane_restr0.0129415
X-RAY DIFFRACTIONf_dihedral_angle_d14.1193819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.41381310.38092490X-RAY DIFFRACTION99.77
2.44-2.630.32461350.32452548X-RAY DIFFRACTION99.19
2.63-2.90.35361330.32522538X-RAY DIFFRACTION99.89
2.9-3.320.33991360.29242573X-RAY DIFFRACTION99.96
3.32-4.180.28381350.23722573X-RAY DIFFRACTION99.49
4.18-44.80.22961440.21912715X-RAY DIFFRACTION99.27
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)
11.4936757092-0.11053341939-0.1321093856090.71899188874-1.198097857815.732695633380.025478075298-0.224023429403-0.191121432573-0.0944448025513-0.2186398466660.2097371979910.0881000643735-0.5237415239660.221838785740.409120546502-0.00105550128639-0.02150383106870.1958135568010.02929423056070.73092275377710.12892985778.3605090165565.8780995855
23.94342820548-0.768520524551-0.7643248606915.426679673554.425864200933.90793438425-0.03048687937530.299950748974-1.072627499510.287337349982-0.5323140753190.9198067220630.615731942764-1.143988908590.4516675017830.683342606538-0.149931829696-0.09950249635790.819658331521-0.1156068639750.8130815897525.644056208993.394787376236.8158739104
31.98038078888-0.589053122481-0.08850385249751.221891256150.2399172165594.37977289520.0610121426757-0.1451407259420.09257641408330.319274390383-0.08489100667560.4099429663440.228118846636-0.1375673350880.05874109832580.464278397958-0.09512909704670.09667076940410.1411603630210.03520450997210.77648183540310.214801422210.532899917766.5175916436
41.89560706507-0.3697583592440.001352730628431.296813908950.8432506705546.94964765707-0.1453808966310.5080618024270.003617364476760.174546741544-0.003890686242210.1842297264391.046017206760.4419024843850.2835391705960.484767107999-0.0244865813511-0.009868053139350.274600883962-0.00322629881770.58287531120112.02634058946.9027342279648.9952391701
51.891085768840.122379091793-0.9680536225191.29871792703-0.3068740383663.470259335520.04159704999320.2151281536890.02710670066080.0976673973295-0.1140287416260.209914764174-0.292978485972-0.03245945518790.1419809338530.3868267601160.008832272283-0.02486450139750.0979203572116-0.03555199785760.6688060737578.5641782700411.432885521457.9840206205
61.500581123070.213854235278-0.6194975083881.821761853310.07602556886913.939191562520.08959065200580.233558146826-0.0927878788595-0.0392837003869-0.1453270818860.0628090484037-0.5889524909740.1975234258220.02767385406140.339960056614-0.0874157340427-0.07960261515020.191681835149-0.003226874324850.70047897497711.605964346610.634834927548.625317974
71.967168032490.162122168838-0.4275943379181.98480020283-1.27892525344.972038707850.1407016491780.24233343232-0.3559524643550.1269505802330.153915060610.411643210002-0.0912837462016-0.0872542508755-0.2891422512670.419265427909-0.00150534475285-0.02991078733320.138515917656-0.03122561025940.6614288205798.668177917389.0062622575359.0323187392
80.276452935163-0.222266370121-0.3783682995971.28937793590.08523213938372.98981743189-0.3125530856270.6257701409680.0642439832373-0.121445207403-0.289224098823-0.507893443973-0.02419233624811.067311085320.4344060727130.602748684888-0.147239075704-0.0361279690681.55420104817-0.03509766761960.72714965835510.50386907673.993511678283.59327872792
90.0406018899934-0.07080330712330.3035366422290.70570837055-0.554393071512.25480330779-0.1548124303680.502924965525-0.2693074917040.097227121250.5497355568820.00991748954449-0.5967063669510.0974473589424-0.4312711610560.7207108966930.0205297521801-0.1663942981471.23317244546-0.08450500764110.7028734217575.334575804737.1950048162615.9933725315
102.2784401767-0.841045573525-0.1362344133892.6055519416-0.2357549008192.20432556867-0.3847647851840.7073365673250.525918033019-0.0179336482450.0805463735022-0.164982772543-0.5981820602590.07322711610560.4290493741450.755928447905-0.101968398619-0.1147535120911.25832854015-0.03065751788220.6441270775689.4359496433413.77250904479.39455506984
110.1502715934470.00468517268494-0.2529822420260.187028065050.221239974114.648236607760.100197848510.3550397671680.6406156742830.3741149698020.1307834126720.130983059136-0.9871606175330.4988795816950.04945251016030.7239201842-0.0947758699645-0.09968459861081.241210563650.007939184769580.64266478058713.399485226911.66269488878.93043716442
120.03625972141470.0782042857251-0.03474959591220.3401696109210.4451514251291.56283619417-0.1174145241840.5730338049890.237248471011-0.3345055351960.141478362321-0.117898193665-0.6383701352950.960631698785-0.230775345230.675686483292-0.124017279618-0.05590095754961.33073304246-0.01613110017730.68073815375215.87042106798.4543862682313.2690943281
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 21 )AA2 - 211 - 20
22chain 'A' and (resid 22 through 34 )AA22 - 3421 - 33
33chain 'A' and (resid 35 through 50 )AA35 - 5034 - 49
44chain 'A' and (resid 51 through 70 )AA51 - 7050 - 69
55chain 'A' and (resid 71 through 111 )AA71 - 11170 - 110
66chain 'A' and (resid 112 through 136 )AA112 - 136111 - 135
77chain 'A' and (resid 137 through 177 )AA137 - 177136 - 176
88chain 'B' and (resid 5 through 20 )BB5 - 201 - 16
99chain 'B' and (resid 21 through 36 )BB21 - 3617 - 32
1010chain 'B' and (resid 37 through 85 )BB37 - 8533 - 81
1111chain 'B' and (resid 86 through 104 )BB86 - 10482 - 100
1212chain 'B' and (resid 105 through 122 )BB105 - 122101 - 118

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