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- PDB-8znu: Catalytic antibody T99_C220A_dP95 -

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Basic information

Entry
Database: PDB / ID: 8znu
TitleCatalytic antibody T99_C220A_dP95
Componentscatalytic antibody T99_C220A_dPro95
KeywordsIMMUNE SYSTEM / Catalytic antibody
Function / homologyCACODYLIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKobayashi, J. / Yoshida, H. / Tsuyuguchi, M. / Kato, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101083 Japan
CitationJournal: Mabs / Year: 2025
Title: Structural and biochemical differences between non-catalytic and catalytic antibodies.
Authors: Uda, T. / Kato, R. / Shigeta, Y. / Hirota, S. / Kobayashi, J. / Yoshida, H. / Tsuyuguchi, M. / Hengphasatporn, K. / Tsujita, M. / Taguchi, H. / Hifumi, E.
History
DepositionMay 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 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: catalytic antibody T99_C220A_dPro95
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2636
Polymers24,6571
Non-polymers6075
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.760, 80.760, 158.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-300-

CAD

21A-448-

HOH

31A-478-

HOH

41A-479-

HOH

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Components

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Antibody , 1 types, 1 molecules A

#1: Antibody catalytic antibody T99_C220A_dPro95


Mass: 24656.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 84 molecules

#2: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE


Mass: 137.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7AsO2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.1 M Sodium cacodylate pH 6.5 36% PEG2000MME

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→42.18 Å / Num. obs: 33164 / % possible obs: 84.8 % / Redundancy: 6.59 % / Biso Wilson estimate: 28.37 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.23 / Net I/σ(I): 5.86
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.702 / Num. unique obs: 2872 / CC1/2: 0.519

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SwissModel

Resolution: 2→42.17 Å / SU ML: 0.2424 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.265 980 5 %
Rwork0.2202 18611 -
obs0.2224 19591 91.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.36 Å2
Refinement stepCycle: LAST / Resolution: 2→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 36 79 1803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00171782
X-RAY DIFFRACTIONf_angle_d0.51892410
X-RAY DIFFRACTIONf_chiral_restr0.0411268
X-RAY DIFFRACTIONf_plane_restr0.0032308
X-RAY DIFFRACTIONf_dihedral_angle_d22.9925259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.33711060.28562016X-RAY DIFFRACTION71.98
2.11-2.240.35451310.27352484X-RAY DIFFRACTION87.05
2.24-2.410.29481430.26262714X-RAY DIFFRACTION94.98
2.41-2.650.34241430.25672730X-RAY DIFFRACTION95.67
2.65-3.040.311480.25522811X-RAY DIFFRACTION96.79
3.04-3.820.2351510.21322855X-RAY DIFFRACTION96.94
3.83-42.170.21351580.17073001X-RAY DIFFRACTION95.27

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