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- PDB-8yj8: Characerization of a novel format scFvXVHH single-chain Biparatop... -

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Basic information

Entry
Database: PDB / ID: 8yj8
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 speciesStreptococcus pyogenes (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 2.0Jun 26, 2024Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Oct 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

Downloads & links

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Assembly

Deposited unit
A: Iron ABC transporter substrate-binding lipoprotein MtsA
B: Iron ABC transporter substrate-binding lipoprotein MtsA
C: VHH43
D: VHH43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8426
Polymers91,7114
Non-polymers1312
Water12,520695
1
A: Iron ABC transporter substrate-binding lipoprotein MtsA
hetero molecules

C: VHH43


Theoretical massNumber of molelcules
Total (without water)45,9213
Polymers45,8562
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
2
B: Iron ABC transporter substrate-binding lipoprotein MtsA
D: VHH43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9213
Polymers45,8562
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)292.931, 58.083, 50.760
Angle α, β, γ (deg.)90.000, 91.240, 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
Components on special symmetry positions
IDModelComponents
11A-522-

HOH

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Components

#1: Protein Iron ABC transporter substrate-binding lipoprotein MtsA


Mass: 31287.549 Da / Num. of mol.: 2
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
#2: Antibody VHH43


Mass: 14567.980 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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M Ammonium sulfate, 20% w/v PEG 3,350

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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 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→48.27 Å / Num. obs: 101614 / % possible obs: 99.3 % / Redundancy: 3.72 % / Biso Wilson estimate: 28.22 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.043 / Net I/σ(I): 8.4
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.69 % / Rmerge(I) obs: 1.116 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3190 / CC1/2: 0.569 / Rpim(I) all: 0.67 / % possible all: 98.05

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HH8

3hh8


Resolution: 1.65→35.57 Å / SU ML: 0.2532 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6728
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2277 5064 4.99 %
Rwork0.1875 96508 -
obs0.1895 101572 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.16 Å2
Refinement stepCycle: LAST / Resolution: 1.65→35.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6288 0 2 695 6985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076480
X-RAY DIFFRACTIONf_angle_d0.86468758
X-RAY DIFFRACTIONf_chiral_restr0.055959
X-RAY DIFFRACTIONf_plane_restr0.00691132
X-RAY DIFFRACTIONf_dihedral_angle_d5.9671874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.39521700.38963016X-RAY DIFFRACTION94.12
1.67-1.690.41251610.37663200X-RAY DIFFRACTION99.79
1.69-1.710.37541700.33533211X-RAY DIFFRACTION99.65
1.71-1.730.31621870.30993160X-RAY DIFFRACTION99.64
1.73-1.760.33141770.29653287X-RAY DIFFRACTION99.88
1.76-1.780.38141700.29183135X-RAY DIFFRACTION99.82
1.78-1.810.30371690.26753264X-RAY DIFFRACTION99.91
1.81-1.830.32281660.25083180X-RAY DIFFRACTION99.82
1.83-1.860.30691570.24873233X-RAY DIFFRACTION99.82
1.86-1.890.26791640.24383231X-RAY DIFFRACTION99.88
1.89-1.920.32591510.2623215X-RAY DIFFRACTION99.64
1.92-1.960.29241680.24463252X-RAY DIFFRACTION99.91
1.96-20.31271560.24533195X-RAY DIFFRACTION99.91
2-2.040.27811760.22033251X-RAY DIFFRACTION99.77
2.04-2.080.23291640.20553236X-RAY DIFFRACTION99.82
2.08-2.130.24821630.1973195X-RAY DIFFRACTION99.82
2.13-2.180.21981540.1973225X-RAY DIFFRACTION99.82
2.18-2.240.21542040.19823202X-RAY DIFFRACTION99.59
2.24-2.310.24081890.19833213X-RAY DIFFRACTION99.77
2.31-2.380.23031490.19243209X-RAY DIFFRACTION99.56
2.38-2.470.26691700.19583216X-RAY DIFFRACTION99.62
2.47-2.570.20461500.19183288X-RAY DIFFRACTION99.59
2.57-2.680.22861880.19823205X-RAY DIFFRACTION99.74
2.68-2.830.21761790.18873221X-RAY DIFFRACTION99.56
2.83-30.24511690.19233250X-RAY DIFFRACTION99.56
3-3.230.22111560.18163245X-RAY DIFFRACTION99.3
3.23-3.560.22481700.16893230X-RAY DIFFRACTION99.27
3.56-4.070.20471830.15273234X-RAY DIFFRACTION99.13
4.07-5.130.15981640.13443287X-RAY DIFFRACTION99.02
5.13-35.570.18921700.16223222X-RAY DIFFRACTION95.74

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