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- PDB-7o52: CD22 d6-d7 in complex with Fab m971 -

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Basic information

Entry
Database: PDB / ID: 7o52
TitleCD22 d6-d7 in complex with Fab m971
Components
  • CD22 d6-d7 Ig domains
  • m971 Fab Heavy chain
  • m971 Fab Light chain
KeywordsIMMUNE SYSTEM / Fab / CD22
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsEreno-Orbea, J. / Sicard, T. / Julien, J.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural details of monoclonal antibody m971 recognition of the membrane-proximal domain of CD22.
Authors: Ereno-Orbea, J. / Liu, X. / Sicard, T. / Kucharska, I. / Li, W. / Borovsky, D. / Cui, H. / Feng, Y. / Dimitrov, D.S. / Julien, J.P.
History
DepositionApr 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: m971 Fab Heavy chain
L: m971 Fab Light chain
U: CD22 d6-d7 Ig domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,03112
Polymers70,0533
Non-polymers9789
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-72 kcal/mol
Surface area27850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.478, 119.719, 241.672
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody m971 Fab Heavy chain


Mass: 24472.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody m971 Fab Light chain


Mass: 23669.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules U

#3: Protein CD22 d6-d7 Ig domains


Mass: 21911.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 45 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.17 Å3/Da / Density % sol: 61.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2M ammonium sulphate, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.41→50 Å / Num. obs: 35031 / % possible obs: 99.6 % / Redundancy: 13.18 % / Biso Wilson estimate: 65.207 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.102 / Χ2: 1.097 / Net I/σ(I): 20.19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.41-2.5512.6241.6811.4654680.5841.75197.4
2.55-2.7313.7211.0292.6852560.861.068100
2.73-2.9513.290.561549170.9460.584100
2.95-3.2313.3360.26810.7845490.9890.278100
3.23-3.613.4910.12621.7441140.9970.131100
3.6-4.1613.3070.0735.3436700.9990.073100
4.16-5.0813.250.04551.9831300.9990.047100
5.08-7.1512.7850.04353.4924580.9990.045100
7.15-7.53111.7980.03466.8114690.9990.03599.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXv1.14refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O4Y

7o4y


Resolution: 2.41→49.823 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.264 --
Rwork0.2257 --
obs-34977 99.46 %
Displacement parametersBiso max: 146.02 Å2 / Biso mean: 69.9446 Å2 / Biso min: 34.61 Å2
Refinement stepCycle: LAST / Resolution: 2.41→49.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 57 37 4746

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