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- PDB-6p4y: Crystal Structure of anti-IL-7Ralpha 4A10 Fab -

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Basic information

Entry
Database: PDB / ID: 6p4y
TitleCrystal Structure of anti-IL-7Ralpha 4A10 Fab
Components
  • 4A10 Fab heavy chain
  • 4A10 Fab light chain
KeywordsIMMUNE SYSTEM / Antibody 4A10 Fab fragment / protein polymer
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsWalsh, S.T.R. / Kashi, L. / Kohnhorst, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Leukemia / Year: 2020
Title: New anti-IL-7R alpha monoclonal antibodies show efficacy against T cell acute lymphoblastic leukemia in pre-clinical models.
Authors: Hixon, J.A. / Andrews, C. / Kashi, L. / Kohnhorst, C.L. / Senkevitch, E. / Czarra, K. / Barata, J.T. / Li, W. / Schneider, J.P. / Walsh, S.T.R. / Durum, S.K.
History
DepositionMay 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 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
H: 4A10 Fab heavy chain
L: 4A10 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,9662
Polymers47,9662
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-25 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.372, 78.496, 69.480
Angle α, β, γ (deg.)90.00, 96.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody 4A10 Fab heavy chain


Mass: 24360.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: mouse hybridoma / Variant: C57BL/6
#2: Antibody 4A10 Fab light chain


Mass: 23606.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Variant: C57BL/6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.03 Å3/Da / Density % sol: 39.33 % / Description: triangular plate
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% PEG 5000, 0.1 M sodium acetate, 20% glycerol, seeded
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2014 / Details: K-B mirrors
RadiationMonochromator: K-B mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.799→39.248 Å / Num. obs: 36735 / % possible obs: 99.1 % / Redundancy: 3.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.1257 / Rpim(I) all: 0.08014 / Rrim(I) all: 0.1495 / Net I/σ(I): 8.33
Reflection shellResolution: 1.799→1.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.418 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 3613 / CC1/2: 0.42 / Rpim(I) all: 0.9215 / Rrim(I) all: 1.418 / % possible all: 96.46

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Processing

Software
NameVersionClassification
PHENIX(1.15_3448: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AE6

1ae6


Resolution: 1.799→39.248 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 1833 5 %
Rwork0.1875 --
obs0.1897 36685 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.799→39.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3326 0 0 243 3569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063410
X-RAY DIFFRACTIONf_angle_d0.924644
X-RAY DIFFRACTIONf_dihedral_angle_d10.0732045
X-RAY DIFFRACTIONf_chiral_restr0.058518
X-RAY DIFFRACTIONf_plane_restr0.006589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7995-1.84810.45241350.43062582X-RAY DIFFRACTION96
1.8481-1.90250.34771400.30962673X-RAY DIFFRACTION100
1.9025-1.96390.2951430.26652721X-RAY DIFFRACTION100
1.9639-2.03410.29941400.22482656X-RAY DIFFRACTION100
2.0341-2.11550.26381420.22422699X-RAY DIFFRACTION100
2.1155-2.21180.26171430.20242696X-RAY DIFFRACTION100
2.2118-2.32840.24541420.18562702X-RAY DIFFRACTION100
2.3284-2.47430.2711420.19632696X-RAY DIFFRACTION100
2.4743-2.66530.24071410.19152680X-RAY DIFFRACTION100
2.6653-2.93340.24931410.18292693X-RAY DIFFRACTION100
2.9334-3.35770.22391420.16952695X-RAY DIFFRACTION99
3.3577-4.22950.18871410.14832663X-RAY DIFFRACTION98
4.2295-39.25730.16271410.15462696X-RAY DIFFRACTION97

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