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- PDB-5nbd: PglK flippase in complex with inhibitory nanobody -

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Basic information

Entry
Database: PDB / ID: 5nbd
TitlePglK flippase in complex with inhibitory nanobody
Components
  • Nanobody
  • WlaB protein
KeywordsTRANSPORT PROTEIN / ABC transporter flippase / nanobody
Function / homology
Function and homology information


ABC-type lipopolysaccharide transporter / lipopolysaccharide floppase activity / protein N-linked glycosylation via asparagine / ATPase-coupled lipid transmembrane transporter activity / protein N-linked glycosylation / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / WlaB protein / Protein glycosylation K
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.9 Å
AuthorsPerez, C. / Pardon, E. / Steyaert, J. / Locher, K.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationSNF 31003AB_131075 and 310030B_166672 Switzerland
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis of inhibition of lipid-linked oligosaccharide flippase PglK by a conformational nanobody.
Authors: Perez, C. / Kohler, M. / Janser, D. / Pardon, E. / Steyaert, J. / Zenobi, R. / Locher, K.P.
History
DepositionMar 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WlaB protein
B: WlaB protein
C: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,1515
Polymers142,2973
Non-polymers8542
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15300 Å2
ΔGint-118 kcal/mol
Surface area57550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.340, 142.660, 199.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein WlaB protein


Mass: 64587.676 Da / Num. of mol.: 2 / Mutation: E510Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: wlaB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O86150, UniProt: Q0P9C4*PLUS
#2: Antibody Nanobody


Mass: 13121.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 4.22 Å3/Da / Density % sol: 70.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.3 / Details: MOPS: NaCl: PEG300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→29.349 Å / Num. all: 307777 / Num. obs: 42284 / % possible obs: 99.87 % / Redundancy: 13.6 % / Biso Wilson estimate: 180.94 Å2 / Rrim(I) all: 0.107 / Net I/σ(I): 13
Reflection shellResolution: 3.9→4 Å / Mean I/σ(I) obs: 1.02 / Num. measured obs: 23226 / Num. unique all: 3161 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C78 and 4UU9

5c78

4uu9


Resolution: 3.9→29.349 Å / SU ML: 0.79 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.65
RfactorNum. reflection% reflection
Rfree0.335 3746 8.87 %
Rwork0.311 --
obs0.313 42249 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 292.21 Å2 / Biso mean: 163.4963 Å2 / Biso min: 89.28 Å2
Refinement stepCycle: final / Resolution: 3.9→29.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10037 0 38 0 10075
Biso mean--202.42 --
Num. residues----1251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310283
X-RAY DIFFRACTIONf_angle_d0.60713861
X-RAY DIFFRACTIONf_chiral_restr0.0381594
X-RAY DIFFRACTIONf_plane_restr0.0031709
X-RAY DIFFRACTIONf_dihedral_angle_d17.2436171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.9-3.94930.4351440.428714391583100
3.9493-4.00110.46531400.417114261566100
4.0011-4.05580.43271400.413714251565100
4.0558-4.11360.39771370.400414071544100
4.1136-4.17480.4071440.397614601604100
4.1748-4.23990.45011440.382214391583100
4.2399-4.30920.39021350.348713941529100
4.3092-4.38320.33681350.345714071542100
4.3832-4.46270.31681450.369914701615100
4.4627-4.54820.3561340.330214011535100
4.5482-4.64070.32141390.328314321571100
4.6407-4.74120.35891390.318114281567100
4.7412-4.8510.3351380.323514091547100
4.851-4.97170.33011430.314714521595100
4.9717-5.10550.35561330.304614221555100
5.1055-5.25490.39071460.319914331579100
5.2549-5.42350.37661350.327714101545100
5.4235-5.6160.43371370.363314251562100
5.616-5.83920.35181360.35481412154899
5.8392-6.10270.42041350.369314291564100
6.1027-6.42130.38261430.369614371580100
6.4213-6.81890.38471350.361314131548100
6.8189-7.33770.31661420.332914191561100
7.3377-8.06220.2831390.294114421581100
8.0622-9.19730.24681370.245614371574100
9.1973-11.47140.25091350.20811400153599
11.4714-29.34970.3431360.3091435157199

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