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- PDB-9fvb: Crystal structure of VcSiaP in complex with a VHH antibody (VHH_VcP#2) -

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Basic information

Entry
Database: PDB / ID: 9fvb
TitleCrystal structure of VcSiaP in complex with a VHH antibody (VHH_VcP#2)
Components
  • Sialic acid-binding periplasmic protein SiaP
  • VHH_VcP#2
KeywordsTRANSPORT PROTEIN / Substrate binding protein / TRAP transporter / VHH antibody / Nanobody
Function / homologyTRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / IMIDAZOLE / TRIETHYLENE GLYCOL / Sialic acid-binding periplasmic protein SiaP
Function and homology information
Biological speciesVibrio cholerae (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSchneberger, N. / Hagelueken, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Commun Biol / Year: 2024
Title: Allosteric substrate release by a sialic acid TRAP transporter substrate binding protein.
Authors: Schneberger, N. / Hendricks, P. / Peter, M.F. / Gehrke, E. / Binder, S.C. / Koenig, P.A. / Menzel, S. / Thomas, G.H. / Hagelueken, G.
History
DepositionJun 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 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

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Assembly

Deposited unit
A: Sialic acid-binding periplasmic protein SiaP
B: Sialic acid-binding periplasmic protein SiaP
C: VHH_VcP#2
H: VHH_VcP#2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,74210
Polymers99,0614
Non-polymers6816
Water8,881493
1
A: Sialic acid-binding periplasmic protein SiaP
C: VHH_VcP#2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8425
Polymers49,5312
Non-polymers3113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sialic acid-binding periplasmic protein SiaP
H: VHH_VcP#2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9005
Polymers49,5312
Non-polymers3693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.296, 50.340, 133.994
Angle α, β, γ (deg.)90.000, 114.880, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein / Antibody , 2 types, 4 molecules ABCH

#1: Protein Sialic acid-binding periplasmic protein SiaP


Mass: 34106.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: siaP, VC_1779 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KR64
#2: Antibody VHH_VcP#2


Mass: 15423.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 499 molecules

#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: Imidazole, MES monohydrate, pH 6.5, PEG 550 MME, PEG 20000, 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol, 1,3-Propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.05→46.38 Å / Num. obs: 57531 / % possible obs: 99.54 % / Redundancy: 2 % / Biso Wilson estimate: 26.91 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.09801 / Net I/σ(I): 7.48
Reflection shellResolution: 2.05→2.13 Å / Rmerge(I) obs: 0.7936 / Num. unique obs: 10986 / CC1/2: 0.436

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→46.38 Å / SU ML: 0.3029 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1329
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2572 1997 3.47 %
Rwork0.1952 55534 -
obs0.1973 57531 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.38 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6647 0 46 493 7186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136825
X-RAY DIFFRACTIONf_angle_d1.20249215
X-RAY DIFFRACTIONf_chiral_restr0.05891003
X-RAY DIFFRACTIONf_plane_restr0.01091194
X-RAY DIFFRACTIONf_dihedral_angle_d9.0488929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.35111340.31353766X-RAY DIFFRACTION94.45
2.1-2.160.31891420.28673939X-RAY DIFFRACTION99.95
2.16-2.220.3321400.27453940X-RAY DIFFRACTION99.95
2.22-2.30.33631430.26663956X-RAY DIFFRACTION99.98
2.3-2.380.30641420.23853933X-RAY DIFFRACTION100
2.38-2.470.31691420.23363940X-RAY DIFFRACTION99.93
2.47-2.590.29571430.21353970X-RAY DIFFRACTION99.98
2.59-2.720.27481420.21343958X-RAY DIFFRACTION100
2.72-2.890.28121430.21413988X-RAY DIFFRACTION99.98
2.89-3.120.28111430.2043976X-RAY DIFFRACTION99.95
3.12-3.430.25571440.18713991X-RAY DIFFRACTION99.88
3.43-3.930.22251440.1644001X-RAY DIFFRACTION99.93
3.93-4.950.21851460.13514036X-RAY DIFFRACTION99.93
4.95-46.380.18471490.15954140X-RAY DIFFRACTION99.84

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