[English] 日本語
Yorodumi
- PDB-5itf: Cetuximab Fab in complex with 2-bromophenylalanine meditope variant -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more