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- PDB-5whj: Crystal structure of Fab fragment of anti-FcRn antibody DX-2507 -

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Basic information

Entry
Database: PDB / ID: 5whj
TitleCrystal structure of Fab fragment of anti-FcRn antibody DX-2507
Components
  • DX-2507 Fab heavy chain
  • DX-2507 Fab light chain
KeywordsIMMUNE SYSTEM / Fabricator / FcRn / B2M / beta-2-microglobulin
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IGL@ protein / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsEdwards, T.E. / Fairman, J.W. / Nixon, A.E. / Kenniston, J.A.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural basis for pH-insensitive inhibition of immunoglobulin G recycling by an anti-neonatal Fc receptor antibody.
Authors: Kenniston, J.A. / Taylor, B.M. / Conley, G.P. / Cosic, J. / Kopacz, K.J. / Lindberg, A.P. / Comeau, S.R. / Atkins, K. / Bullen, J. / TenHoor, C. / Adelman, B.A. / Sexton, D.J. / Edwards, T.E. / Nixon, A.E.
History
DepositionJul 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: DX-2507 Fab heavy chain
L: DX-2507 Fab light chain


Theoretical massNumber of molelcules
Total (without water)45,6422
Polymers45,6422
Non-polymers00
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-22 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.170, 116.170, 79.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11L-356-

HOH

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Components

#1: Antibody DX-2507 Fab heavy chain


Mass: 22981.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: S6BAN1
#2: Antibody DX-2507 Fab light chain


Mass: 22659.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGL@ / Production host: Homo sapiens (human) / References: UniProt: Q6NS95
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: DX-2507 Fab at 9.5 mg/mL against Morpheus screen condition G5 with 10% PEG 20000, 20% PEG 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.15→50.01 Å / Num. obs: 29879 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 42.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.061 / Χ2: 1.001 / Net I/σ(I): 23.8 / Num. measured all: 218958 / Scaling rejects: 3
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 378 / CC1/2: 1 / Rrim(I) all: 0.022 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(dev_2863)refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IDX

3idx


Resolution: 2.15→41.072 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 1439 4.82 %RANDOM
Rwork0.1798 ---
obs0.1821 29840 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→41.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3091 0 0 255 3346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073176
X-RAY DIFFRACTIONf_angle_d0.8384345
X-RAY DIFFRACTIONf_dihedral_angle_d4.9882175
X-RAY DIFFRACTIONf_chiral_restr0.055495
X-RAY DIFFRACTIONf_plane_restr0.005562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1499-2.22670.2431280.20872824X-RAY DIFFRACTION100
2.2267-2.31590.26971420.20822807X-RAY DIFFRACTION100
2.3159-2.42130.29331550.21122802X-RAY DIFFRACTION100
2.4213-2.54890.25271430.20712817X-RAY DIFFRACTION100
2.5489-2.70860.28271470.20822817X-RAY DIFFRACTION100
2.7086-2.91770.30171300.20752850X-RAY DIFFRACTION100
2.9177-3.21120.27051300.2112845X-RAY DIFFRACTION100
3.2112-3.67560.24371500.18512855X-RAY DIFFRACTION99
3.6756-4.62980.17111520.13982852X-RAY DIFFRACTION98
4.6298-41.07980.18181620.15932932X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5148-0.63270.55331.1245-0.12851.25360.0808-0.1847-0.1846-0.05580.096-0.10480.4586-0.3614-0.00010.3444-0.0536-0.01890.32280.02210.2366-37.5403-10.18814.073
21.58580.00760.55841.7076-0.21450.4408-0.0202-0.3497-0.07840.11380.169-0.35840.1718-0.27210.00060.2813-0.0240.00690.34980.01830.1883-39.9993-6.3445.4131
30.1710.0352-0.11270.02790.04940.41310.57340.40720.4039-0.70890.14970.2949-0.5409-0.09820.17310.67520.13430.06740.53660.06340.2467-53.471619.2948-25.2615
41.48170.3394-0.58451.3209-0.00530.87590.08390.08020.0016-0.12550.0071-0.017-0.1792-0.19870.00020.21160.03260.02020.2793-0.02780.1892-50.739711.04-16.6061
52.29610.653-0.47152.6725-0.15551.2704-0.3454-0.1925-0.57010.2604-0.0135-0.59140.1242-0.146-0.03040.2079-0.03830.06140.2667-0.06430.5344-17.867-1.3335-3.4501
61.7876-0.33760.51650.48910.06521.1180.05380.0875-0.09260.1530.02220.0271-0.26870.0303-0.00120.21160.00950.04950.2088-0.02150.277-37.149613.6068-9.5339
71.68740.8953-0.21370.6714-0.81462.60120.16770.05850.69230.4104-0.03820.1477-0.9180.21640.00330.4963-0.06090.05550.2985-0.01020.43-42.65827.1312-14.4811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 61 )
2X-RAY DIFFRACTION2chain 'H' and (resid 62 through 122 )
3X-RAY DIFFRACTION3chain 'H' and (resid 123 through 137 )
4X-RAY DIFFRACTION4chain 'H' and (resid 138 through 217 )
5X-RAY DIFFRACTION5chain 'L' and (resid 2 through 93 )
6X-RAY DIFFRACTION6chain 'L' and (resid 94 through 133 )
7X-RAY DIFFRACTION7chain 'L' and (resid 134 through 212 )

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