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- PDB-8yj5: Characerization of a novel format scFvXVHH single-chain Biparatop... -

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Basic information

Entry
Database: PDB / ID: 8yj5
TitleCharacerization of a novel format scFvXVHH single-chain Biparatopic antibody against a metal binding protein, MtsA
Components
  • Iron ABC transporter substrate-binding lipoprotein MtsA
  • VHH43
KeywordsMETAL TRANSPORT/IMMUNE SYSTEM / Antibody / Metal Transport / METAL TRANSPORT-IMMUNE SYSTEM complex
Function / homology
Function and homology information


iron ion transport / cell adhesion / metal ion binding / plasma membrane
Similarity search - Function
Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Iron ABC transporter substrate-binding lipoprotein MtsA
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Streptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.66 Å
AuthorsIto, S. / Nagatoishi, S. / Nakakido, M. / Tsumoto, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H05766 Japan
CitationJournal: Protein Sci. / Year: 2024
Title: Characterization of a novel format scFv×VHH single-chain biparatopic antibody against metal binding protein MtsA.
Authors: Asano, R. / Takeuchi, M. / Nakakido, M. / Ito, S. / Aikawa, C. / Yokoyama, T. / Senoo, A. / Ueno, G. / Nagatoishi, S. / Tanaka, Y. / Nakagawa, I. / Tsumoto, K.
History
DepositionMar 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: VHH43
A: Iron ABC transporter substrate-binding lipoprotein MtsA


Theoretical massNumber of molelcules
Total (without water)45,7682
Polymers45,7682
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.450, 120.450, 156.176
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody VHH43


Mass: 14567.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein Iron ABC transporter substrate-binding lipoprotein MtsA


Mass: 31200.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: mtsA, SPy_0453, M5005_Spy0368 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A4G4
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: 6.19 Å3/Da / Density % sol: 80.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 1.8 M Ammonium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Nov 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.66→47.79 Å / Num. obs: 12349 / % possible obs: 99.94 % / Redundancy: 7.61 % / Biso Wilson estimate: 156.82 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.069 / Net I/σ(I): 7.9
Reflection shellResolution: 3.66→3.79 Å / Rmerge(I) obs: 1.891 / Mean I/σ(I) obs: 1 / Num. unique obs: 3077 / CC1/2: 0.452 / Rpim(I) all: 0.746

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Processing

Software
NameVersionClassification
PHENIX1.17_3644+SVNrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HH8

3hh8


Resolution: 3.66→47.79 Å / SU ML: 0.5996 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.4238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3033 582 4.71 %
Rwork0.2631 11779 -
obs0.2651 12361 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 106.97 Å2
Refinement stepCycle: LAST / Resolution: 3.66→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3141 0 0 0 3141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02283204
X-RAY DIFFRACTIONf_angle_d2.03664329
X-RAY DIFFRACTIONf_chiral_restr0.1179475
X-RAY DIFFRACTIONf_plane_restr0.0091558
X-RAY DIFFRACTIONf_dihedral_angle_d11.71781189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.66-4.020.41991120.3672977X-RAY DIFFRACTION99.74
4.02-4.60.36711630.30542910X-RAY DIFFRACTION100
4.61-5.80.28021630.26292925X-RAY DIFFRACTION100
5.8-47.790.27221440.22982967X-RAY DIFFRACTION100

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