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- PDB-9fzc: Structure of OmpA-short in complex with nanobody Nb01 -

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Basic information

Entry
Database: PDB / ID: 9fzc
TitleStructure of OmpA-short in complex with nanobody Nb01
Components
  • Nanobody 01
  • Outer membrane protein A
KeywordsMEMBRANE PROTEIN / Porin / Nanobody / Complex
Function / homology
Function and homology information


outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / porin activity / pore complex / monoatomic ion transport / cell outer membrane / outer membrane-bounded periplasmic space / symbiont entry into host cell ...outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / porin activity / pore complex / monoatomic ion transport / cell outer membrane / outer membrane-bounded periplasmic space / symbiont entry into host cell / DNA damage response / identical protein binding / membrane
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
N-OCTANE / Outer membrane protein A
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein A
B: Outer membrane protein A
C: Nanobody 01
D: Nanobody 01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,92423
Polymers64,9024
Non-polymers2,02219
Water4,972276
1
A: Outer membrane protein A
C: Nanobody 01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1769
Polymers32,4512
Non-polymers7257
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer membrane protein A
D: Nanobody 01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,74814
Polymers32,4512
Non-polymers1,29712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.048, 55.296, 107.805
Angle α, β, γ (deg.)90.000, 91.090, 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-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 0 through 171 or resid 207 through 213))
d_1ens_2chain "C"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERALAALAAA0 - 1712 - 173
d_12ens_1OCTOCTOCTOCTAE201
d_13ens_1OCTOCTOCTOCTAF202
d_14ens_1OCTOCTOCTOCTAG203
d_15ens_1OCTOCTOCTOCTBL201
d_16ens_1OCTOCTOCTOCTAH204
d_17ens_1OCTOCTOCTOCTAI205
d_18ens_1OCTOCTOCTOCTAJ206
d_21ens_1SERSERALAALABB0 - 1712 - 173
d_22ens_1OCTOCTOCTOCTBM202
d_23ens_1OCTOCTOCTOCTBN203
d_24ens_1OCTOCTOCTOCTBO204
d_25ens_1OCTOCTOCTOCTBP205
d_26ens_1OCTOCTOCTOCTBQ206
d_27ens_1OCTOCTOCTOCTBR207
d_28ens_1OCTOCTOCTOCTBS208
d_11ens_2VALVALVALVALCC5 - 1215 - 121
d_21ens_2VALVALVALVALDD5 - 1215 - 121

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999943594219, 0.00731466498908, -0.00770091266254), (-0.00726451748465, -0.999952358049, -0.00651984803505), (-0.00774823628019, -0.00646353686325, 0.999949092467)26.4658034994, 32.0746062696, 0.157241767332
2given(-0.993223419497, -0.0837531150951, -0.0805770108378), (0.0866116047228, -0.995706873811, -0.0326535047692), (-0.0774962508191, -0.0394111298779, 0.996213377721)28.1843885358, 32.5284148686, 0.124394395649

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Components

#1: Protein Outer membrane protein A / OmpA / Outer membrane porin A / Outer membrane protein 3A / Outer membrane protein B / Outer ...OmpA / Outer membrane porin A / Outer membrane protein 3A / Outer membrane protein B / Outer membrane protein II* / Outer membrane protein d


Mass: 18992.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: ompA, con, tolG, tut, b0957, JW0940 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): MC1061 / References: UniProt: P0A910
#2: Antibody Nanobody 01 / Nb01


Mass: 13458.021 Da / Num. of mol.: 2
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: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C8H18
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium acetate pH 5.5, 0.2 M calcium acetate, 25 % PEG MME 2K

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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 PILATUS 2M-F / Detector: PIXEL / Date: Feb 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→107.79 Å / Num. obs: 30638 / % possible obs: 100 % / Redundancy: 6.76 % / Biso Wilson estimate: 30.62 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.146 / Net I/σ(I): 10.7
Reflection shellResolution: 2.275→2.314 Å / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1534 / CC1/2: 0.696

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→107.79 Å / SU ML: 0.2609 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3869
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 1531 5 %
Rwork0.2076 29094 -
obs0.209 30625 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.85 Å2
Refinement stepCycle: LAST / Resolution: 2.27→107.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 138 276 4898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224719
X-RAY DIFFRACTIONf_angle_d0.59446346
X-RAY DIFFRACTIONf_chiral_restr0.0445644
X-RAY DIFFRACTIONf_plane_restr0.0036816
X-RAY DIFFRACTIONf_dihedral_angle_d13.72361717
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS3.83806346599
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS0.527165627034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.350.31231360.25772603X-RAY DIFFRACTION99.89
2.35-2.430.29351390.2392641X-RAY DIFFRACTION99.96
2.43-2.530.26031390.22582643X-RAY DIFFRACTION100
2.53-2.640.27951380.23142615X-RAY DIFFRACTION100
2.64-2.780.28081380.22262626X-RAY DIFFRACTION99.89
2.78-2.960.26921390.22882632X-RAY DIFFRACTION99.93
2.96-3.190.23181380.20352626X-RAY DIFFRACTION99.96
3.19-3.510.19761400.19522651X-RAY DIFFRACTION99.96
3.51-4.010.21841410.18442666X-RAY DIFFRACTION99.93
4.02-5.060.17021390.16522656X-RAY DIFFRACTION99.89
5.06-107.790.26481440.24272735X-RAY DIFFRACTION99.69
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)
10.609543924350.03895061723250.3510597684880.8157279542210.2832343033143.424497724910.001327144898830.0282917979716-0.0233465348506-0.03783352514780.0158256997606-0.056502377160.02790952029410.148453518426-0.02627606998720.149472402533-0.00389482934576-0.005421718172470.17013396493-0.002145161549180.2277233986141.445086422414.7151306424945.6888193483
20.7889817121720.13669638873-0.9205783307450.722444309551-0.4333044081242.4545129212-0.002649556191370.0945437363119-0.0449035560671-0.04429932648090.00624598595025-0.008538092207680.0115505026328-0.1298300685830.004842557989710.140747633192-0.00111690957558-0.05354969589980.151346927479-0.003478171238110.1996863156324.598333026326.807988346345.7652908397
32.63089315035-0.3428741328240.4194110231182.104103973670.8217776826771.831853417760.05427479778880.26182659275-0.203555583617-0.1015024856890.01043933819240.1097094240.169469801837-0.0670562894572-0.0889891876150.318607008926-0.00906866674903-0.03289816500590.2661597144870.008191924447330.210450106413-4.38739282527-0.1986789195222.54777722591
42.14191503753-0.125701515425-1.047740546142.46791563258-1.637556895452.08463171127-0.03481372299240.1733615221870.126617611839-0.182067994615-0.0802217729564-0.111686402146-0.141566965504-0.07752071937030.1046444317250.352395471329-0.014988577034-0.01258195285780.279365046063-0.002445341057070.24641594015532.351961133632.26088289273.01097934723
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 0 through 171)AA0 - 1711 - 172
22(chain 'B' and resid 0 through 171)BI0 - 1711 - 172
33(chain 'C' and resid 5 through 121)CT5 - 1211 - 117
44(chain 'D' and resid 5 through 121)DU5 - 1211 - 117

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