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- PDB-6ugu: Crystal structure of the Fab fragment of anti-TNFa antibody infli... -

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Basic information

Entry
Database: PDB / ID: 6ugu
TitleCrystal structure of the Fab fragment of anti-TNFa antibody infliximab (Remicade) in a C-centered orthorhombic crystal form, Lot C
Components
  • PF06438179 Fab Heavy Chain
  • PF06438179 Fab Light Chain
KeywordsIMMUNE SYSTEM / antibody / Fab / infliximab / biosimilar / TNFa
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / : / 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 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / IGK@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLerch, T.F. / Sharpe, P. / Mayclin, S.J. / Edwards, T.E. / Polleck, S. / Rouse, J.C. / Conlan, H.D.
CitationJournal: BioDrugs / Year: 2020
Title: Crystal Structures of PF-06438179/GP1111, an Infliximab Biosimilar.
Authors: Lerch, T.F. / Sharpe, P. / Mayclin, S.J. / Edwards, T.E. / Polleck, S. / Rouse, J.C. / Zou, Q. / Conlon, H.D.
History
DepositionSep 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: PF06438179 Fab Heavy Chain
L: PF06438179 Fab Light Chain
A: PF06438179 Fab Heavy Chain
B: PF06438179 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)95,6344
Polymers95,6344
Non-polymers00
Water15,763875
1
H: PF06438179 Fab Heavy Chain
L: PF06438179 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)47,8172
Polymers47,8172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-25 kcal/mol
Surface area19490 Å2
MethodPISA
2
A: PF06438179 Fab Heavy Chain
B: PF06438179 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)47,8172
Polymers47,8172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-25 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.260, 138.150, 195.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody PF06438179 Fab Heavy Chain


Mass: 24356.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: A8K008
#2: Antibody PF06438179 Fab Light Chain


Mass: 23460.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: Q6P5S8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / 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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 mg/mL PF06438179 Fab lot C against Wiz 34 screen condition B4 (20% PEG3350, 0.2 M potassium citrate tribasic), supplemented with 20% ethylene glycol as cryoprotectant, crystal tracking ID ...Details: 10 mg/mL PF06438179 Fab lot C against Wiz 34 screen condition B4 (20% PEG3350, 0.2 M potassium citrate tribasic), supplemented with 20% ethylene glycol as cryoprotectant, crystal tracking ID 267668b4, unique puck ID sdw5-4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 19, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 59825 / % possible obs: 99.5 % / Redundancy: 6.272 % / Biso Wilson estimate: 33.543 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.101 / Χ2: 0.972 / Net I/σ(I): 17.28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.266.2880.63.2943920.850.655100
2.26-2.326.2940.5133.8342870.890.56100
2.32-2.396.3010.4654.1741750.9030.507100
2.39-2.466.3060.394.9640440.9320.425100
2.46-2.546.3150.3146.1539340.9530.34299.9
2.54-2.636.3050.2467.6438140.9710.26899.8
2.63-2.736.2990.2088.9136800.980.22799.8
2.73-2.846.3250.16711.0335290.9860.18299.7
2.84-2.976.3070.13313.3933790.9910.14699.7
2.97-3.116.2960.10417.0532630.9930.11499.7
3.11-3.286.2830.0821.2430900.9960.08799.5
3.28-3.486.2990.06425.7529230.9980.0799.4
3.48-3.726.2410.05330.4827580.9980.05899.4
3.72-4.026.2480.04634.4525710.9980.05199.2
4.02-4.46.2540.03840.3723510.9990.04198.8
4.4-4.926.2080.03444.4921490.9990.03798.5
4.92-5.686.2280.03442.7718950.9990.03798.5
5.68-6.966.1920.03739.2716120.9990.04197.8
6.96-9.846.0440.02944.712610.9990.03197.8
9.84-505.5450.02648.577180.9990.02994.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX2229refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4G3Y

4g3y


Resolution: 2.2→50 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.1
RfactorNum. reflection% reflection
Rfree0.2185 2898 4.85 %
Rwork0.17 --
obs0.1724 59813 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.17 Å2 / Biso mean: 29.9191 Å2 / Biso min: 11.24 Å2
Refinement stepCycle: final / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6506 0 0 876 7382
Biso mean---35.79 -
Num. residues----863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076691
X-RAY DIFFRACTIONf_angle_d0.839125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
2.2-2.23610.27471400.210226730100
2.2361-2.27470.30751190.202827400100
2.2747-2.3160.25771450.206326640100
2.316-2.36060.23731470.208426930100
2.3606-2.40870.33281350.216427100100
2.4087-2.46110.2691370.202926810100
2.4611-2.51840.26161310.198926960100
2.5184-2.58130.24961320.186726940100
2.5813-2.65110.25181450.192127160100
2.6511-2.72910.23311460.188126890100
2.7291-2.81720.2561320.189227450100
2.8172-2.91790.29081160.196727040100
2.9179-3.03470.26171250.199727050100
3.0347-3.17280.2481280.185227020100
3.1728-3.340.20981450.173726990100
3.34-3.54920.20491790.16542701099
3.5492-3.82310.19151510.16042687099
3.8231-4.20770.17411400.13812703099
4.2077-4.8160.14791310.11532765099
4.816-6.06570.17361290.13562731098
6.0657-500.21211450.16673817097

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