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- PDB-5vh5: Crystal Structure of Fc fragment of anti-TNFa antibody infliximab -

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Basic information

Entry
Database: PDB / ID: 5vh5
TitleCrystal Structure of Fc fragment of anti-TNFa antibody infliximab
ComponentsInfliximab Fc
KeywordsIMMUNE SYSTEM / antibody / Fc / biosimilar / Infliximab / TNFa / anti-TNFa
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsMayclin, S.J. / Edwards, T.E. / Lerch, T.F. / Conlan, H. / Sharpe, P.
CitationJournal: MAbs / Year: 2017
Title: Infliximab crystal structures reveal insights into self-association.
Authors: Lerch, T.F. / Sharpe, P. / Mayclin, S.J. / Edwards, T.E. / Lee, E. / Conlon, H.D. / Polleck, S. / Rouse, J.C. / Luo, Y. / Zou, Q.
History
DepositionApr 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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_conn_type / 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 / _chem_comp.type / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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: Infliximab Fc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0396
Polymers28,3611
Non-polymers1,6785
Water3,387188
1
A: Infliximab Fc
hetero molecules

A: Infliximab 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_554-x,y,-z-1/21
Buried area6960 Å2
ΔGint-169 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.160, 148.030, 75.900
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-779-

HOH

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Components

#1: Protein Infliximab Fc


Mass: 28361.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Humanized / Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Cricetulus griseus (Chinese hamster)
#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)-[beta-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[LFucpb1-6]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-1b_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)][b-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.: 188 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: JCSG+ E7 (266855e7): 10% propanol-2, 200mM zinc acetate, 100mM sodium cacodylate pH6.5: protein conc. 10mg/mL: cryo 20% ethylene glycol: puckID sxt1-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 22, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.75→33.264 Å / Num. obs: 28936 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.985 % / Biso Wilson estimate: 24.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.06 / Χ2: 1.008 / Net I/σ(I): 17.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.86.1450.5443.3213010211721170.8660.595100
1.8-1.846.1650.4044.3812724206420640.930.442100
1.84-1.96.1620.35.7912294199619950.9590.32899.9
1.9-1.966.1710.2297.6112083195819580.9730.251100
1.96-2.026.1860.179.8211661188518850.9850.186100
2.02-2.096.1670.1312.111329183718370.9910.142100
2.09-2.176.1280.11213.9610878177517750.9930.123100
2.17-2.266.1090.09916.5610257167916790.9920.108100
2.26-2.366.130.08617.7210084164516450.9960.095100
2.36-2.476.0310.07420.229451156715670.9960.081100
2.47-2.616.0160.06522.669066150715070.9960.071100
2.61-2.775.9580.0625.498437141614160.9960.065100
2.77-2.965.8450.05327.867780133113310.9970.058100
2.96-3.25.750.04630.427164124612460.9980.051100
3.2-3.55.6490.04232.646541115811580.9980.046100
3.5-3.915.6390.04233.485960105710570.9980.046100
3.91-4.525.5560.03734.7251509289270.9980.0499.9
4.52-5.535.5160.03634.7344248038020.9980.0499.9
5.53-7.835.3380.03734.0933846356340.9980.04199.8
7.83-33.2644.4940.03931.7815103783360.9970.04488.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.63 Å33.77 Å
Translation4.63 Å33.77 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
Cootmodel building
PHENIXdev_2229refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4cdh
Resolution: 1.75→33.264 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.74
RfactorNum. reflection% reflection
Rfree0.2282 1447 5 %
Rwork0.1904 --
obs0.1923 28932 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.08 Å2 / Biso mean: 39.7069 Å2 / Biso min: 11.37 Å2
Refinement stepCycle: final / Resolution: 1.75→33.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 103 188 1886
Biso mean--57.39 37.32 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071778
X-RAY DIFFRACTIONf_angle_d0.8562444
X-RAY DIFFRACTIONf_chiral_restr0.054298
X-RAY DIFFRACTIONf_plane_restr0.005300
X-RAY DIFFRACTIONf_dihedral_angle_d14.1361083
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.81250.29491440.250227212865100
1.8125-1.88510.27231420.232327022844100
1.8851-1.97090.29451420.210727122854100
1.9709-2.07480.25041440.195727222866100
2.0748-2.20480.23271430.199727212864100
2.2048-2.3750.22711450.201327512896100
2.375-2.61390.26961430.200927342877100
2.6139-2.99190.25721460.200727592905100
2.9919-3.76860.23491470.183327882935100
3.7686-33.27010.17711510.16922875302699
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.0512-0.1409-0.17820.0357-0.01220.53160.0178-0.9471.07420.37830.0909-0.131-0.35530.1597-0.0040.3558-0.0353-0.07850.3922-0.40330.59229.507723.1671-4.9949
20.8813-0.02280.06270.78320.48320.3772-0.0399-0.58321.35620.28570.3673-0.355-0.4249-0.16221.29960.40620.0041-0.10170.0466-0.57350.60046.422625.8396-5.9977
31.3350.6357-0.39970.63990.15090.49580.0192-0.5087-0.92330.09-0.0472-0.03040.07220.1249-0.06930.20120.0078-0.00570.2940.14320.320818.9534-5.5661-12.3139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 241 through 282 )A241 - 282
2X-RAY DIFFRACTION2chain 'A' and (resid 283 through 339 )A283 - 339
3X-RAY DIFFRACTION3chain 'A' and (resid 340 through 446 )A340 - 446

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