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- PDB-9vx2: Crystal structure of the apo form of HisMab-1 Fab -

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Basic information

Entry
Database: PDB / ID: 9vx2
TitleCrystal structure of the apo form of HisMab-1 Fab
Components
  • HisMab-1 immunoglobulin heavy chain variable region
  • HisMab-1 immunoglobulin light chain variable region
KeywordsIMMUNE SYSTEM / Fab / HisMab-1 / His-tag
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsHoshi, S. / Arimori, T. / Harada-Hikita, A.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21H02416 Japan
Japan Society for the Promotion of Science (JSPS)JP25K02215 Japan
Japan Agency for Medical Research and Development (AMED)JP24am0521010 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121001 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101083 Japan
CitationJournal: J.Mol.Biol. / Year: 2025
Title: Functional and Structural Characterization of a Novel Anti-His-tag Antibody, HisMab-1.
Authors: Hitomi, N. / Hoshi, S. / Kaneko, M.K. / Kato, R. / Iwasaki, K. / Takagi, J. / Kato, Y. / Harada-Hikita, A. / Arimori, T.
History
DepositionJul 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HisMab-1 immunoglobulin heavy chain variable region
B: HisMab-1 immunoglobulin light chain variable region
C: HisMab-1 immunoglobulin heavy chain variable region
D: HisMab-1 immunoglobulin light chain variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,97910
Polymers96,4034
Non-polymers5766
Water1,20767
1
A: HisMab-1 immunoglobulin heavy chain variable region
B: HisMab-1 immunoglobulin light chain variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5866
Polymers48,2012
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-65 kcal/mol
Surface area20040 Å2
MethodPISA
2
C: HisMab-1 immunoglobulin heavy chain variable region
D: HisMab-1 immunoglobulin light chain variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3944
Polymers48,2012
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-44 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.719, 191.099, 177.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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Components

#1: Antibody HisMab-1 immunoglobulin heavy chain variable region


Mass: 24081.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Monoclonal antibody / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCAG-Neo / Cell line (production host): ExpiCHO-S / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): ExpiCHO-S
#2: Antibody HisMab-1 immunoglobulin light chain variable region


Mass: 24119.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Monoclonal antibody / Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): ExpiCHO-S / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): ExpiCHO-S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0M ammonium sulphate, 0.1M Tris-HCl (pH 7.0), 0.1M lithium sulfate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.052 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 11, 2022
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.052 Å / Relative weight: 1
ReflectionResolution: 2.39→48.2 Å / Num. obs: 49897 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Net I/σ(I): 17.1
Reflection shellResolution: 2.39→2.47 Å / Rmerge(I) obs: 1.145 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4539 / CC1/2: 0.946

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→48.2 Å / SU ML: 0.4008 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.1589
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2884 2547 5.11 %
Rwork0.2315 47309 -
obs0.2344 49856 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.85 Å2
Refinement stepCycle: LAST / Resolution: 2.39→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6607 0 30 67 6704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00876784
X-RAY DIFFRACTIONf_angle_d1.01889236
X-RAY DIFFRACTIONf_chiral_restr0.05311045
X-RAY DIFFRACTIONf_plane_restr0.00761170
X-RAY DIFFRACTIONf_dihedral_angle_d18.04192414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.440.45731580.39172554X-RAY DIFFRACTION99.23
2.44-2.490.45941490.38122571X-RAY DIFFRACTION99.42
2.49-2.540.4351270.35212596X-RAY DIFFRACTION99.27
2.54-2.60.40661370.32652585X-RAY DIFFRACTION99.56
2.6-2.660.36991370.28732614X-RAY DIFFRACTION99.64
2.66-2.740.34451260.2782629X-RAY DIFFRACTION99.67
2.74-2.820.37861260.28352612X-RAY DIFFRACTION99.74
2.82-2.910.34461200.29072628X-RAY DIFFRACTION99.75
2.91-3.010.3351390.2942620X-RAY DIFFRACTION99.67
3.01-3.130.35451440.30822586X-RAY DIFFRACTION99.82
3.13-3.270.34131360.26962621X-RAY DIFFRACTION99.93
3.27-3.450.34391590.25832623X-RAY DIFFRACTION99.86
3.45-3.660.31210.23232675X-RAY DIFFRACTION99.82
3.66-3.950.27421610.22322607X-RAY DIFFRACTION99.93
3.95-4.340.22151570.18732636X-RAY DIFFRACTION99.96
4.34-4.970.21841380.16882666X-RAY DIFFRACTION100
4.97-6.260.23611600.18082680X-RAY DIFFRACTION100
6.26-48.20.24451520.18872806X-RAY DIFFRACTION99.66

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