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- PDB-6ugw: Crystal structure of the Fc fragment of PF06438179/GP1111 an infl... -

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Entry
Database: PDB / ID: 6ugw
TitleCrystal structure of the Fc fragment of PF06438179/GP1111 an infliximab biosimilar in a C-centered orthorhombic crystal form, Lot A
ComponentsPF-06438179/GP1111 Fc
KeywordsIMMUNE SYSTEM / Antibody / biologic / biosimilar / infliximab / fragment crystallizable
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 subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
ACETATE ION / Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMayclin, S.J. / Edwards, T.E.
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: Data collection / Database references / Category: chem_comp / citation
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PF-06438179/GP1111 Fc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0396
Polymers28,3611
Non-polymers1,6785
Water2,738152
1
A: PF-06438179/GP1111 Fc
hetero molecules

A: PF-06438179/GP1111 Fc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,07812
Polymers56,7232
Non-polymers3,35510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area7770 Å2
ΔGint-77 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.090, 148.090, 75.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-503-

ZN

21A-745-

HOH

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Components

#1: Protein PF-06438179/GP1111 Fc


Mass: 28361.252 Da / Num. of mol.: 1 / Fragment: LotA_Fc
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: P0DOX5
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1422.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4-5/a4-b1_a6-h1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL protein with JCSG+ E7 (266849e7): 10% 2-propanol, 200 mM zinc acetate, 100 mM sodium cacodylate, pH 6.5, cryoprotectant: 20% ethylene glycol, puckID kux1-2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 5, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19460 / % possible obs: 99.9 % / Redundancy: 6.103 % / Biso Wilson estimate: 27.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.091 / Χ2: 0.971 / Net I/σ(I): 13.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.056.1760.4973.6914170.8830.543100
2.05-2.116.180.3914.6213800.9380.426100
2.11-2.176.1960.3425.2413490.9470.374100
2.17-2.246.190.2756.4612900.9570.399.9
2.24-2.316.1970.2586.8912820.9610.282100
2.31-2.396.1780.2127.9912190.9790.231100
2.39-2.486.2030.1849.1311820.9810.20199.9
2.48-2.586.1610.15610.3711510.9880.17199.9
2.58-2.76.1670.13112.4111030.9890.143100
2.7-2.836.170.10914.3710450.9930.119100
2.83-2.986.1430.0916.6610120.9940.099100
2.98-3.166.0970.07519.49670.9950.082100
3.16-3.386.1260.06322.798830.9970.06999.8
3.38-3.656.0390.05725.278470.9960.06299.8
3.65-46.0340.05625.787700.9970.06199.7
4-4.475.980.05128.317140.9980.05699.6
4.47-5.165.9250.04928.546260.9970.05399.8
5.16-6.325.780.05228.135460.9960.05799.5
6.32-8.945.5910.05328.644280.9970.05899.8
8.94-504.7590.05426.792490.9940.0695.8

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Processing

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

4cdh


Resolution: 2→50 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.45
RfactorNum. reflection% reflection
Rfree0.2189 972 5 %
Rwork0.1807 --
obs0.1825 19450 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.46 Å2 / Biso mean: 42.2573 Å2 / Biso min: 13.37 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 103 152 1862
Biso mean--57.98 38.72 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071771
X-RAY DIFFRACTIONf_angle_d0.8912431
X-RAY DIFFRACTIONf_chiral_restr0.054294
X-RAY DIFFRACTIONf_plane_restr0.005299
X-RAY DIFFRACTIONf_dihedral_angle_d15.1631069
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.10540.28021370.2112590100
2.1054-2.23730.23891370.19652597100
2.2373-2.410.23521370.19392619100
2.41-2.65240.23171370.1932621100
2.6524-3.03610.22891390.19422635100
3.0361-3.82440.2141400.18262651100
3.8244-500.19381450.1586276599
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)
10.24690.96490.09944.8424-0.37641.34790.1455-0.72510.58360.7097-0.1529-0.2441-0.25040.09250.00160.3314-0.01-0.070.4151-0.22770.448410.520517.2204-5.4923
20.64520.59490.44180.52590.39740.30070.1094-0.30110.77150.28060.149-0.259-0.54840.04830.6230.5449-0.0943-0.11430.2257-0.69440.98539.531432.0399-2.4616
31.61840.84530.41730.51820.56921.97370.0807-0.56420.86050.3975-0.0576-0.0135-0.152-0.10260.19920.28710.0154-0.02920.3443-0.20540.3423.575615.8775-4.6525
40.52441.50760.03344.64740.78631.7266-0.006-0.08831.2817-0.2340.11880.1079-0.8031-0.08720.14950.49520.0255-0.03390.2643-0.13640.86144.194928.6211-11.5912
56.5581-2.53310.82552.9476-0.48281.2460.1727-0.0096-0.8227-0.1571-0.2215-0.25840.20850.1083-0.01680.1841-0.00120.00080.20740.06040.300819.1925-6.2366-16.5769
61.48690.3277-0.34321.73750.09532.6613-0.0381-0.7159-0.82850.1946-0.0158-0.06880.03750.093-0.01490.20280.0205-0.01360.45090.16670.220621.6275-4.0111-11.2895
73.3058-1.18010.94911.1128-0.59121.0918-0.2051-0.851-1.0090.1315-0.2951-0.34490.14260.2943-0.0720.31560.02720.00710.41480.25710.395213.8393-8.5087-8.1238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 240 through 267 )A240 - 267
2X-RAY DIFFRACTION2chain 'A' and (resid 268 through 304 )A268 - 304
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 317 )A305 - 317
4X-RAY DIFFRACTION4chain 'A' and (resid 318 through 339 )A318 - 339
5X-RAY DIFFRACTION5chain 'A' and (resid 340 through 375 )A340 - 375
6X-RAY DIFFRACTION6chain 'A' and (resid 376 through 421 )A376 - 421
7X-RAY DIFFRACTION7chain 'A' and (resid 422 through 446 )A422 - 446

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