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- PDB-8yj6: Characerization of a novel format scFvXVHH single-chain Biparatop... -

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Basic information

Entry
Database: PDB / ID: 8yj6
TitleCharacerization of a novel format scFvXVHH single-chain Biparatopic antibody against a metal binding protein, MtsA
ComponentsIron ABC transporter substrate-binding lipoprotein MtsA
KeywordsMETAL TRANSPORT / Antibody
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.37 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Iron ABC transporter substrate-binding lipoprotein MtsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2662
Polymers31,2001
Non-polymers651
Water8,773487
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)39.935, 49.828, 147.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M MgCl2, 0.1 M Tris (pH 8.5), 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1.282 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: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.37→38.55 Å / Num. obs: 54591 / % possible obs: 87.42 % / Redundancy: 12.3 % / Biso Wilson estimate: 10.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Net I/σ(I): 21
Reflection shellResolution: 1.37→1.42 Å / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 592 / CC1/2: 0.727 / Rpim(I) all: 0.343

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Processing

Software
NameVersionClassification
PHENIX1.17_3644+SVNrefinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.37→38.55 Å / SU ML: 0.1193 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.8478
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1937 2757 5.07 %
Rwork0.1699 97842 -
obs0.1711 54591 86.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.84 Å2
Refinement stepCycle: LAST / Resolution: 1.37→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 1 487 2676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532241
X-RAY DIFFRACTIONf_angle_d0.82073024
X-RAY DIFFRACTIONf_chiral_restr0.0784333
X-RAY DIFFRACTIONf_plane_restr0.0055385
X-RAY DIFFRACTIONf_dihedral_angle_d16.9616852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.5141590.44031020X-RAY DIFFRACTION27.13
1.39-1.40.3723640.3391355X-RAY DIFFRACTION36.61
1.4-1.420.2751090.3031636X-RAY DIFFRACTION42.96
1.42-1.440.3398880.27451836X-RAY DIFFRACTION49.57
1.44-1.460.30451090.23892160X-RAY DIFFRACTION57.27
1.46-1.480.26171300.2122423X-RAY DIFFRACTION64.15
1.48-1.50.19081450.20312588X-RAY DIFFRACTION70.77
1.5-1.520.21981660.19272980X-RAY DIFFRACTION78.08
1.52-1.550.20921690.1853257X-RAY DIFFRACTION86.25
1.55-1.570.20231780.17383493X-RAY DIFFRACTION93.6
1.57-1.60.18121980.1653819X-RAY DIFFRACTION99.65
1.6-1.630.21272060.16583679X-RAY DIFFRACTION100
1.63-1.660.18291870.16623787X-RAY DIFFRACTION100
1.66-1.690.19161910.17233724X-RAY DIFFRACTION100
1.69-1.730.20651660.1683853X-RAY DIFFRACTION100
1.73-1.770.19312040.1673716X-RAY DIFFRACTION100
1.77-1.810.18751890.17343765X-RAY DIFFRACTION100
1.81-1.860.20831740.17943753X-RAY DIFFRACTION100
1.86-1.920.20032060.16823789X-RAY DIFFRACTION100
1.92-1.980.17962130.16543711X-RAY DIFFRACTION100
1.98-2.050.18452180.16523752X-RAY DIFFRACTION100
2.05-2.130.16922170.1653753X-RAY DIFFRACTION100
2.13-2.230.19512390.16443723X-RAY DIFFRACTION100
2.23-2.350.17482340.16323720X-RAY DIFFRACTION100
2.35-2.490.18991670.16873803X-RAY DIFFRACTION100
2.49-2.690.16711990.16563733X-RAY DIFFRACTION100
2.69-2.960.20461920.18023742X-RAY DIFFRACTION100
2.96-3.390.24462000.16833773X-RAY DIFFRACTION100
3.39-4.260.18312020.14993745X-RAY DIFFRACTION100
4.26-38.550.15632030.15153754X-RAY DIFFRACTION99.85

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