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- PDB-5itf: Cetuximab Fab in complex with 2-bromophenylalanine meditope variant -

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Basic information

Entry
Database: PDB / ID: 5itf
TitleCetuximab Fab in complex with 2-bromophenylalanine meditope variant
Components
  • Cetuximab Fab, heavy chain
  • Cetuximab Fab, light chain
  • Meditope variant
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsBzymek, K.P. / Williams, J.C.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope-Fab complexes.
Authors: Bzymek, K.P. / Avery, K.A. / Ma, Y. / Horne, D.A. / Williams, J.C.
History
DepositionMar 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 2.0Dec 13, 2017Group: Atomic model / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / pdbx_struct_oper_list
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_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Mar 28, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_sheet_hbond / pdbx_validate_close_contact ...pdbx_struct_sheet_hbond / pdbx_validate_close_contact / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Revision 2.2Sep 27, 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 2.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _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: Cetuximab Fab, light chain
B: Cetuximab Fab, heavy chain
C: Cetuximab Fab, light chain
D: Cetuximab Fab, heavy chain
E: Meditope variant
F: Meditope variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,32510
Polymers96,9456
Non-polymers3804
Water6,648369
1
A: Cetuximab Fab, light chain
B: Cetuximab Fab, heavy chain
E: Meditope variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6635
Polymers48,4733
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cetuximab Fab, light chain
D: Cetuximab Fab, heavy chain
F: Meditope variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6635
Polymers48,4733
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.010, 82.210, 211.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Cetuximab Fab, light chain


Mass: 23287.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS, HOMO SAPIENS / Production host: unidentified (others)
#2: Antibody Cetuximab Fab, heavy chain


Mass: 23725.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS, HOMO SAPIENS / Production host: unidentified (others)
#3: Protein/peptide Meditope variant


Mass: 1459.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M citric acid, 0.1 M sodium hydrogen phosphate, 0.4 M potassium hydrogen phosphate, 1.6 M sodium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.51→34.136 Å / Num. obs: 38574 / % possible obs: 98.5 % / Redundancy: 4.1 % / Net I/σ(I): 25.2
Reflection shellResolution: 2.51→2.58 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 6.5 / % possible all: 92.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GW1

4gw1


Resolution: 2.51→34.136 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.58
RfactorNum. reflection% reflection
Rfree0.223 1929 5 %
Rwork0.1835 --
obs0.1855 38565 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.51→34.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6725 0 20 369 7114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036943
X-RAY DIFFRACTIONf_angle_d0.5979470
X-RAY DIFFRACTIONf_dihedral_angle_d10.2814121
X-RAY DIFFRACTIONf_chiral_restr0.0441063
X-RAY DIFFRACTIONf_plane_restr0.0041213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5101-2.57280.31511280.22852428X-RAY DIFFRACTION92
2.5728-2.64230.26041340.22492558X-RAY DIFFRACTION99
2.6423-2.72010.27941360.22322583X-RAY DIFFRACTION99
2.7201-2.80780.29761370.22092594X-RAY DIFFRACTION99
2.8078-2.90810.28061370.21242611X-RAY DIFFRACTION99
2.9081-3.02450.2611370.21372589X-RAY DIFFRACTION99
3.0245-3.16210.24871380.2112635X-RAY DIFFRACTION99
3.1621-3.32860.24761360.20812584X-RAY DIFFRACTION99
3.3286-3.5370.21741390.18662642X-RAY DIFFRACTION99
3.537-3.80970.22991370.18422590X-RAY DIFFRACTION98
3.8097-4.19250.20071380.15142639X-RAY DIFFRACTION99
4.1925-4.79780.15671410.13282673X-RAY DIFFRACTION99
4.7978-6.03920.17941420.15052696X-RAY DIFFRACTION99
6.0392-34.13890.21341490.19482814X-RAY DIFFRACTION98
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)
11.48720.45190.65252.2163-1.13952.76060.3818-0.1260.29440.2709-0.02720.3124-0.61910.0683-0.38870.4973-0.04640.14080.3541-0.16720.4334-6.8991-25.5483-14.9628
20.62020.5046-0.20841.4936-1.812.24640.4108-0.23960.35840.4774-0.0470.5852-0.62030.3575-0.28260.432-0.02810.11830.2909-0.08440.3473-6.3411-25.9616-22.5087
31.85310.11761.12025.41053.15295.42720.04650.15810.17210.12440.0875-0.04640.26180.0436-0.11820.1553-0.01990.01790.2089-0.01590.3568-3.5966-30.8389-53.2133
43.1089-0.46313.38760.87311.41958.1869-0.1246-0.15220.5185-0.0519-0.37030.1489-0.01520.1860.61680.1679-0.041-0.00640.3060.04070.4315-12.1916-33.5177-55.2266
53.2924-0.05760.50841.97880.97784.42770.09360.28860.1821-0.0289-0.07870.24450.18560.0393-0.01510.1586-0.0230.01160.17860.00210.2996-5.3663-28.3306-54.51
63.73721.67661.59752.99520.71786.6257-0.0430.5419-0.3836-0.3030.1018-0.09330.6410.7209-0.00910.33860.1691-0.01940.3579-0.01820.35383.0392-49.8947-25.6814
72.06880.54640.09282.3003-0.33054.73870.1175-0.4463-0.195-0.0295-0.0512-0.01360.21040.3669-0.01090.3027-0.0046-0.03840.3349-0.04280.2350.5852-47.5889-14.6998
82.07810.51610.29311.07961.06444.04390.0669-0.0564-0.01850.0625-0.1106-0.07060.2003-0.1319-0.03120.1970.0768-0.0390.1056-0.0390.30122.698-41.0403-37.8498
91.96011.449-0.58084.2051-0.84211.9841-0.0567-0.21830.1122-0.05650.00120.06110.00230.00830.05380.150.005-0.00880.255-0.070.2534.4208-35.5624-44.6287
103.00542.9078-1.79647.1383-3.00543.7508-0.0858-0.6857-0.07250.052-0.3035-0.72140.00540.5330.22730.18940.0169-0.02980.3088-0.03190.315912.421-39.0448-43.9061
113.7172.1629-1.34547.7426-3.30574.8994-0.1953-0.1363-0.3652-0.6127-0.1614-0.25040.57770.6220.25620.18860.01620.02730.2937-0.04050.330112.7865-40.072-49.9386
127.90227.07745.18239.53046.31644.20660.7419-0.881-0.91940.1229-0.1741-0.87460.3071-0.2139-0.5530.40860.10460.00260.42920.08010.3932-20.1848-16.5948-17.5991
132.2810.5793-0.72521.99591.43742.91620.0234-0.2887-0.27780.02790.0825-0.01410.4048-0.001-0.16050.39750.0119-0.010.35160.11410.3397-29.003-13.7968-11.6611
140.83320.48490.70460.19791.03023.64310.0832-0.2617-0.22850.16980.0107-0.16730.27640.0723-0.02330.40330.06560.00160.28490.07650.2876-26.1508-13.506-20.8986
152.55970.7524-0.83442.20331.06462.30630.03460.63670.2528-0.56780.00350.3463-0.161-0.3603-0.00750.1716-0.0048-0.04080.34020.04350.2963-34.36070.0998-55.4125
160.92131.409-1.58349.9287-8.16487.4568-0.0458-0.2217-0.07240.09430.0020.00930.00850.36420.14040.1583-0.023-0.0340.1881-0.01950.2139-25.2191-10.228-48.7434
173.2941.9198-2.84253.0576-1.96192.4525-0.00220.1244-0.040.20360.1230.04170.0277-0.1583-0.03090.1513-0.0373-0.0190.2537-0.00060.2458-25.0565-9.5014-44.7869
181.85370.3982-0.39335.6807-3.2014.4745-0.06730.4325-0.1572-0.5564-0.0932-0.14110.317-0.01640.10550.156-0.01810.04260.2873-0.04350.2305-25.7379-6.7777-57.7835
196.05593.3606-5.16755.2203-4.84847.2896-0.20890.2637-0.0156-0.00290.2119-0.284-0.5145-0.7256-0.0030.40260.05590.05680.34-0.04920.298-34.948710.7641-22.5837
201.18220.3223-0.47421.49260.14724.6493-0.0723-0.49310.2742-0.0730.06230.1276-0.3059-0.1485-0.00550.35930.0931-0.00010.3683-0.05820.2508-32.83956.9549-12.8126
213.2893-0.27730.63890.7824-1.63143.4353-0.3417-0.18620.3318-0.60040.02950.5417-0.8245-0.16740.13580.16990.04120.05370.16680.03890.1968-35.02925.0298-46.0454
222.71341.5231.11135.0370.87742.4763-0.0505-0.2961-0.0769-0.0486-0.05460.2693-0.0936-0.25240.0930.14480.0330.0260.20870.02950.2353-39.1961-0.7985-43.3419
235.1165-2.77953.39026.0799-0.88749.7814-0.2302-0.2061-1.1935-0.32680.6172-0.2850.1365-0.5276-0.52360.3971-0.03860.00470.2777-0.0010.4953-8.2847-35.971-29.841
244.47050.6445-1.02519.41261.26170.6496-0.4742-0.8065-0.3038-1.0886-0.00950.12810.3880.3830.45170.63490.06020.12550.5126-0.00580.3174-23.9733-3.4861-28.2694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 113 )
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 150 )
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 163 )
5X-RAY DIFFRACTION5chain 'A' and (resid 164 through 213 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 17 )
7X-RAY DIFFRACTION7chain 'B' and (resid 18 through 105 )
8X-RAY DIFFRACTION8chain 'B' and (resid 106 through 140 )
9X-RAY DIFFRACTION9chain 'B' and (resid 141 through 196 )
10X-RAY DIFFRACTION10chain 'B' and (resid 197 through 209 )
11X-RAY DIFFRACTION11chain 'B' and (resid 210 through 220 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 25 )
13X-RAY DIFFRACTION13chain 'C' and (resid 26 through 75 )
14X-RAY DIFFRACTION14chain 'C' and (resid 76 through 113 )
15X-RAY DIFFRACTION15chain 'C' and (resid 114 through 128 )
16X-RAY DIFFRACTION16chain 'C' and (resid 129 through 150 )
17X-RAY DIFFRACTION17chain 'C' and (resid 151 through 174 )
18X-RAY DIFFRACTION18chain 'C' and (resid 175 through 213 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 17 )
20X-RAY DIFFRACTION20chain 'D' and (resid 18 through 117 )
21X-RAY DIFFRACTION21chain 'D' and (resid 118 through 140 )
22X-RAY DIFFRACTION22chain 'D' and (resid 141 through 220 )
23X-RAY DIFFRACTION23chain 'E' and (resid 1 through 12 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 12 )

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