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- PDB-6pe7: Crystal Structure of ABBV-323 FAB -

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Basic information

Entry
Database: PDB / ID: 6pe7
TitleCrystal Structure of ABBV-323 FAB
Components
  • FAB Heavy ChainFragment antigen-binding
  • FAB Light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / CD40 / FAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsArgiriadi, M.A.
CitationJournal: BMC Mol Cell Biol / Year: 2019
Title: CD40/anti-CD40 antibody complexes which illustrate agonist and antagonist structural switches.
Authors: Argiriadi, M.A. / Benatuil, L. / Dubrovska, I. / Egan, D.A. / Gao, L. / Greischar, A. / Hardman, J. / Harlan, J. / Iyer, R.B. / Judge, R.A. / Lake, M. / Perron, D.C. / Sadhukhan, R. / ...Authors: Argiriadi, M.A. / Benatuil, L. / Dubrovska, I. / Egan, D.A. / Gao, L. / Greischar, A. / Hardman, J. / Harlan, J. / Iyer, R.B. / Judge, R.A. / Lake, M. / Perron, D.C. / Sadhukhan, R. / Sielaff, B. / Sousa, S. / Wang, R. / McRae, B.L.
History
DepositionJun 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / software
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: FAB Heavy Chain
L: FAB Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2324
Polymers48,0402
Non-polymers1922
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-52 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.654, 130.375, 132.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody FAB Heavy Chain / Fragment antigen-binding


Mass: 23748.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody FAB Light chain / Fragment antigen-binding


Mass: 24290.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion
Details: 25% (w/v) PMME 550, 0.1M MES pH 6.5, 0.01M zinc sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→57.2 Å / Num. obs: 56956 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 1 / Net I/σ(I): 25.5
Reflection shellResolution: 1.74→1.75 Å / Num. unique obs: 545 / CC1/2: 0.793

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QOS

3qos
PDB Unreleased entry


Resolution: 1.74→24.356 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 22.71 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2299 2724 4.79 %
Rwork0.1961 --
obs0.1977 56858 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→24.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 10 394 3682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053409
X-RAY DIFFRACTIONf_angle_d0.8654642
X-RAY DIFFRACTIONf_dihedral_angle_d2.8952417
X-RAY DIFFRACTIONf_chiral_restr0.054516
X-RAY DIFFRACTIONf_plane_restr0.005594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.77160.30381500.31362847X-RAY DIFFRACTION100
1.7716-1.80570.35851580.28042775X-RAY DIFFRACTION100
1.8057-1.84250.28171450.27792800X-RAY DIFFRACTION100
1.8425-1.88260.34331390.26762815X-RAY DIFFRACTION100
1.8826-1.92640.28621400.24992821X-RAY DIFFRACTION100
1.9264-1.97450.27381450.22982829X-RAY DIFFRACTION100
1.9745-2.02790.25691260.21742835X-RAY DIFFRACTION100
2.0279-2.08750.2771360.21012821X-RAY DIFFRACTION100
2.0875-2.15490.24951410.21472832X-RAY DIFFRACTION100
2.1549-2.23180.2171380.20352838X-RAY DIFFRACTION100
2.2318-2.32110.22811420.20262846X-RAY DIFFRACTION100
2.3211-2.42670.20871700.20392823X-RAY DIFFRACTION100
2.4267-2.55450.24341500.20032837X-RAY DIFFRACTION100
2.5545-2.71430.26291360.19542846X-RAY DIFFRACTION100
2.7143-2.92360.24981400.19782863X-RAY DIFFRACTION100
2.9236-3.21720.24521270.19922894X-RAY DIFFRACTION100
3.2172-3.68140.23641460.18372876X-RAY DIFFRACTION100
3.6814-4.63290.18141400.16212916X-RAY DIFFRACTION100
4.6329-24.3580.19221550.1833020X-RAY DIFFRACTION100

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