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- PDB-7o4y: m971 Fab in complex with anti-Kappa VHH domain -

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Basic information

Entry
Database: PDB / ID: 7o4y
Titlem971 Fab in complex with anti-Kappa VHH domain
Components
  • Anti-Kappa VHH domain
  • m971 Fab heavy chain
  • m971 Fab light chain
KeywordsIMMUNE SYSTEM / Fab / CD22
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
K: Anti-Kappa VHH domain
H: m971 Fab heavy chain
L: m971 Fab light chain


Theoretical massNumber of molelcules
Total (without water)59,4683
Polymers59,4683
Non-polymers00
Water10,845602
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-26 kcal/mol
Surface area25010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.998, 73.998, 98.808
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Antibody Anti-Kappa VHH domain


Mass: 11326.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: 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)
#3: 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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M lithium acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.6→39.127 Å / Num. obs: 79907 / % possible obs: 99.8 % / Redundancy: 4.129 % / Biso Wilson estimate: 28.661 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.051 / Χ2: 1.016 / Net I/σ(I): 17.31 / Num. measured all: 329897
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.73.9690.5372.365100512930128520.7770.6299.4
1.7-1.814.0510.3124.154940912202121970.9180.36100
1.81-1.964.1670.1627.734688211261112510.9780.18699.9
1.96-2.144.1170.09213.44278710397103920.9910.106100
2.14-2.44.2010.06319.1939586943194230.9960.07399.9
2.4-2.764.1870.04525.8934784830983080.9970.052100
2.76-3.384.2790.0337.8330192705870560.9990.034100
3.38-4.764.1570.02548.0122545542954240.9990.02899.9
4.76-39.1274.230.02750.9212707301430040.9980.03199.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ANI

6ani


Resolution: 1.6→39.127 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 26.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 2024 2.54 %
Rwork0.2191 77769 -
obs0.2198 79793 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.45 Å2 / Biso mean: 24.8029 Å2 / Biso min: 12.52 Å2
Refinement stepCycle: final / Resolution: 1.6→39.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 0 602 4626
Biso mean---32.32 -
Num. residues----553
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.6-1.640.2931460.28045505
1.64-1.68440.28511440.26635600
1.6844-1.73390.28621420.25455539
1.7339-1.78990.28641400.24945554
1.7899-1.85390.28241460.24495593
1.8539-1.92810.28171470.23575524
1.9281-2.01580.26651500.22515548
2.0158-2.12210.25371430.22225575
2.1221-2.2550.29991440.22595548
2.255-2.42910.26321350.22895553
2.4291-2.67350.28051460.2385587
2.6735-3.06030.24461410.22185557
3.0603-3.85510.20131420.19815572
3.8551-3.9790.21941580.19635514

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