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- PDB-9udp: Single-chain Fv antibody of B2 -

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Basic information

Entry
Database: PDB / ID: 9udp
TitleSingle-chain Fv antibody of B2
ComponentsSingle-chain Fv antibody of B2
KeywordsIMMUNE SYSTEM / ANTIGEN BINDING / AFFINITY MATURATION / SOMATIC HYPERMUTATION
Function / homologyFORMIC ACID
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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

Downloads & links

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Assembly

Deposited unit
A: Single-chain Fv antibody of B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2187
Polymers25,8041
Non-polymers4146
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-0 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.762, 71.956, 81.289
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: Antibody Single-chain Fv antibody of B2


Mass: 25803.545 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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 4.0 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 39699 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 14.29 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.2
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1911 / CC1/2: 0.756 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→31.99 Å / SU ML: 0.1137 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.145
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1743 1982 5 %
Rwork0.1556 37641 -
obs0.1565 39623 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.58 Å2
Refinement stepCycle: LAST / Resolution: 1.48→31.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 27 223 1999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811991
X-RAY DIFFRACTIONf_angle_d1.07222726
X-RAY DIFFRACTIONf_chiral_restr0.099300
X-RAY DIFFRACTIONf_plane_restr0.0083348
X-RAY DIFFRACTIONf_dihedral_angle_d14.2928731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.520.23791380.22782609X-RAY DIFFRACTION99.96
1.52-1.560.23961390.20742658X-RAY DIFFRACTION100
1.56-1.60.21041410.19312664X-RAY DIFFRACTION100
1.6-1.660.21031380.18212646X-RAY DIFFRACTION99.93
1.66-1.710.20551410.17162653X-RAY DIFFRACTION99.93
1.71-1.780.17311400.162658X-RAY DIFFRACTION99.93
1.78-1.860.20961400.14852664X-RAY DIFFRACTION99.93
1.86-1.960.17021400.13992680X-RAY DIFFRACTION100
1.96-2.090.14731410.13462668X-RAY DIFFRACTION99.89
2.09-2.250.15891420.1422682X-RAY DIFFRACTION99.96
2.25-2.470.1611430.14792715X-RAY DIFFRACTION100
2.47-2.830.17471430.14732730X-RAY DIFFRACTION100
2.83-3.570.15031440.14532738X-RAY DIFFRACTION100
3.57-31.990.17731520.16122876X-RAY DIFFRACTION99.84
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5238885193250.1993998900380.01467021467880.4773330054040.390566615030.6893105254470.03581966242450.0343648812812-0.0301765499056-0.0622498919859-0.01080694215390.00934867450308-0.02895013905240.009046293241370.0002145140110120.1126844718510.00895545913524-0.007450798241920.100966539687-0.004732724004280.1036827541414.85653328399.0313860712723.9291852776
20.49356003494-0.2260335746810.07031270042320.9612412459170.2364822896320.833327668554-0.0328768960374-0.02377744964950.004291549948880.0196876394888-0.01475143235880.009769643347670.0268364083277-0.0219991439017-0.002620274250910.0967143980024-0.009933851648160.009296827563570.10774702245-0.008859198944760.10146712275512.7985681971-6.8148288251910.4268118764
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 112 )2 - 1121 - 111
22chain 'A' and (resid 128 through 245 )128 - 245112 - 229

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