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- PDB-9udo: Single-chain Fv antibody of F8 complex with NNP-Cap -

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Basic information

Entry
Database: PDB / ID: 9udo
TitleSingle-chain Fv antibody of F8 complex with NNP-Cap
ComponentsSingle-chain Fv antibody of F8
KeywordsIMMUNE SYSTEM / ANTIGEN BINDING / AFFINITY MATURATION / SOMATIC HYPERMUTATION
Function / homology:
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsYoshida, M. / Hanazono, Y. / Numoto, N. / Ito, N. / Oda, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis of anti-(4-hydroxy-3-nitrophenyl)acetyl antibodies during affinity maturation
Authors: Yoshida, M. / Hanazono, Y. / Numoto, N. / Yabuno, S. / Ito, N. / Azuma, T. / Oda, M.
History
DepositionApr 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Single-chain Fv antibody of F8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2382
Polymers25,8811
Non-polymers3571
Water2,738152
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)136.770, 34.950, 46.210
Angle α, β, γ (deg.)90.000, 99.260, 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-520-

HOH

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Components

#1: Antibody Single-chain Fv antibody of F8


Mass: 25880.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-A1L81 / 6-[2-(3,5-dinitro-4-oxidanyl-phenyl)ethanoylamino]hexanoic acid


Mass: 357.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N3O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6 M sodium citrate tribasic dihydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 17379 / % possible obs: 97.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 23.17 Å2 / Rmerge(I) obs: 0.282 / Net I/σ(I): 4.5
Reflection shellResolution: 1.88→1.99 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.924 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2707 / CC1/2: 0.433 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→40.97 Å / SU ML: 0.2483 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2508 865 5 %
Rwork0.2207 16427 -
obs0.2222 17292 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.87 Å2
Refinement stepCycle: LAST / Resolution: 1.88→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 25 152 1959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341881
X-RAY DIFFRACTIONf_angle_d0.72912563
X-RAY DIFFRACTIONf_chiral_restr0.0493277
X-RAY DIFFRACTIONf_plane_restr0.0075328
X-RAY DIFFRACTIONf_dihedral_angle_d16.4609661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-20.32911410.28882688X-RAY DIFFRACTION95.41
2-2.150.31171440.26752723X-RAY DIFFRACTION97.32
2.15-2.370.3031440.25022732X-RAY DIFFRACTION97.79
2.37-2.710.26671460.23142778X-RAY DIFFRACTION98.29
2.71-3.420.25541450.21862757X-RAY DIFFRACTION97.25
3.42-40.970.1991450.18472749X-RAY DIFFRACTION94.24

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