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- PDB-8znt: Catalytic antibody T99_C220A -

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Basic information

Entry
Database: PDB / ID: 8znt
TitleCatalytic antibody T99_C220A
ComponentsCatalytic antibody T99_C220A
KeywordsIMMUNE SYSTEM / Catalytic antibody
Function / homology: / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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

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Assembly

Deposited unit
A: Catalytic antibody T99_C220A
B: Catalytic antibody T99_C220A
C: Catalytic antibody T99_C220A
D: Catalytic antibody T99_C220A
E: Catalytic antibody T99_C220A
F: Catalytic antibody T99_C220A
G: Catalytic antibody T99_C220A
H: Catalytic antibody T99_C220A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,44595
Polymers198,0298
Non-polymers5,41687
Water2,864159
1
A: Catalytic antibody T99_C220A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,46112
Polymers24,7541
Non-polymers70711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catalytic antibody T99_C220A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,27911
Polymers24,7541
Non-polymers52510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Catalytic antibody T99_C220A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,35511
Polymers24,7541
Non-polymers60110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Catalytic antibody T99_C220A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,36012
Polymers24,7541
Non-polymers60711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Catalytic antibody T99_C220A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,54213
Polymers24,7541
Non-polymers78912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Catalytic antibody T99_C220A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,41511
Polymers24,7541
Non-polymers66110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Catalytic antibody T99_C220A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,74115
Polymers24,7541
Non-polymers98714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Catalytic antibody T99_C220A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,29310
Polymers24,7541
Non-polymers5399
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.085, 85.326, 104.580
Angle α, β, γ (deg.)106.772, 91.437, 116.914
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Antibody , 1 types, 8 molecules ABCDEFGH

#1: Antibody
Catalytic antibody T99_C220A


Mass: 24753.621 Da / Num. of mol.: 8
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 , 6 types, 246 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 14%(w/v) PG3350, 0.4 M KSCN, 0.1 M HEPES(pH7.5), 30%(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 66456 / % possible obs: 98.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 46.34 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.078 / Net I/σ(I): 22.7
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.444 / Num. unique obs: 3335 / CC1/2: 0.878 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HCR

4hcr


Resolution: 2.61→28.11 Å / SU ML: 0.3572 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 27.8719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2542 3229 4.86 %
Rwork0.1945 63167 -
obs0.1974 66396 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.62 Å2
Refinement stepCycle: LAST / Resolution: 2.61→28.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13389 0 320 159 13868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002513926
X-RAY DIFFRACTIONf_angle_d0.567718793
X-RAY DIFFRACTIONf_chiral_restr0.04272079
X-RAY DIFFRACTIONf_plane_restr0.00312405
X-RAY DIFFRACTIONf_dihedral_angle_d18.62441979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.650.3341270.26132300X-RAY DIFFRACTION82.44
2.65-2.690.33041280.26692751X-RAY DIFFRACTION97.83
2.69-2.740.34191270.25452775X-RAY DIFFRACTION98.27
2.74-2.780.39591490.2562730X-RAY DIFFRACTION98.16
2.78-2.830.33891440.24362789X-RAY DIFFRACTION98.39
2.83-2.890.2941200.22932739X-RAY DIFFRACTION98.01
2.89-2.950.29511340.23342797X-RAY DIFFRACTION98.29
2.95-3.010.28121500.2292734X-RAY DIFFRACTION98.36
3.01-3.080.29021550.22062762X-RAY DIFFRACTION98.55
3.08-3.160.28461400.20572753X-RAY DIFFRACTION98.6
3.16-3.240.27741320.20862761X-RAY DIFFRACTION98.74
3.24-3.340.2811490.20692760X-RAY DIFFRACTION98.61
3.34-3.450.2581480.20062766X-RAY DIFFRACTION98.55
3.45-3.570.2451340.19392780X-RAY DIFFRACTION98.78
3.57-3.710.25341640.19252761X-RAY DIFFRACTION98.82
3.71-3.880.24631460.18962808X-RAY DIFFRACTION98.99
3.88-4.080.25461380.18322742X-RAY DIFFRACTION98.94
4.08-4.340.23761250.17032789X-RAY DIFFRACTION98.98
4.34-4.670.18381260.15362781X-RAY DIFFRACTION99.05
4.67-5.140.22281410.16152810X-RAY DIFFRACTION99.19
5.14-5.880.23581750.17732729X-RAY DIFFRACTION98.94
5.88-7.380.25511320.20852756X-RAY DIFFRACTION98.03
7.38-28.110.21191450.17932794X-RAY DIFFRACTION99.26

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