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- PDB-9fvc: Crystal structure of VcSiaP in complex with a VHH antibody (VHH_VcP#1) -

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Basic information

Entry
Database: PDB / ID: 9fvc
TitleCrystal structure of VcSiaP in complex with a VHH antibody (VHH_VcP#1)
Components
  • Sialic acid-binding periplasmic protein SiaP
  • VHH_VcP#2
KeywordsTRANSPORT PROTEIN / Substrate binding protein / TRAP transporter / VHH antibody / Nanobody / Complex
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 / Sialic acid-binding periplasmic protein SiaP
Function and homology information
Biological speciesVibrio cholerae (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)99,1674
Polymers99,1674
Non-polymers00
Water1,02757
1
A: Sialic acid-binding periplasmic protein SiaP
H: VHH_VcP#2


Theoretical massNumber of molelcules
Total (without water)49,5842
Polymers49,5842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sialic acid-binding periplasmic protein SiaP
C: VHH_VcP#2


Theoretical massNumber of molelcules
Total (without water)49,5842
Polymers49,5842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.607, 72.366, 85.604
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Sialic acid-binding periplasmic protein SiaP


Mass: 33790.371 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: 15793.354 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)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: Tris BICINE, pH 8.5, PEG 550 MME, PEG 20000, Sodium fluoride, Sodium bromide, Sodium iodide

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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: 2.64→47.18 Å / Num. obs: 31540 / % possible obs: 99.61 % / Redundancy: 2 % / Biso Wilson estimate: 35.22 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.09713 / Net I/σ(I): 6.9
Reflection shellResolution: 2.64→2.71 Å / Rmerge(I) obs: 0.5301 / Num. unique obs: 2153 / CC1/2: 0.623

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Processing

Software
NameVersionClassification
PHENIXv1.20.1-4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→47.18 Å / SU ML: 0.2764 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9258
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2537 2000 6.35 %
Rwork0.2205 29516 -
obs0.2229 31516 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.83 Å2
Refinement stepCycle: LAST / Resolution: 2.64→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6648 0 0 57 6705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00696780
X-RAY DIFFRACTIONf_angle_d0.839176
X-RAY DIFFRACTIONf_chiral_restr0.04211010
X-RAY DIFFRACTIONf_plane_restr0.0091192
X-RAY DIFFRACTIONf_dihedral_angle_d16.10962504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.710.34421370.29782004X-RAY DIFFRACTION95.33
2.71-2.780.34851410.29032083X-RAY DIFFRACTION99.96
2.78-2.860.36261400.29662070X-RAY DIFFRACTION99.95
2.86-2.960.37131420.30052099X-RAY DIFFRACTION100
2.96-3.060.31821400.2942077X-RAY DIFFRACTION99.82
3.06-3.190.35061420.27412084X-RAY DIFFRACTION100
3.19-3.330.32411410.25542091X-RAY DIFFRACTION100
3.33-3.510.31821420.24132103X-RAY DIFFRACTION99.91
3.51-3.730.25171430.22482098X-RAY DIFFRACTION100
3.73-4.010.23791430.19622113X-RAY DIFFRACTION100
4.01-4.420.21430.16642105X-RAY DIFFRACTION99.96
4.42-5.050.15581440.16122144X-RAY DIFFRACTION99.96
5.06-6.370.22571480.18572169X-RAY DIFFRACTION100
6.37-47.180.16491540.18092276X-RAY DIFFRACTION99.71

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