[English] 日本語
Yorodumi
- PDB-3c08: Crystal structure the Fab fragment of matuzumab/EMD72000 (Fab72000) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c08
TitleCrystal structure the Fab fragment of matuzumab/EMD72000 (Fab72000)
Components
  • Matuzumab Fab Heavy chain
  • Matuzumab Fab Light chain
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / ANTITUMOR / DRUG
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsFerguson, K.M. / Schmiedel, J. / Knoechel, T.
CitationJournal: Cancer Cell / Year: 2008
Title: Matuzumab binding to EGFR prevents the conformational rearrangement required for dimerization.
Authors: Schmiedel, J. / Blaukat, A. / Li, S. / Knochel, T. / Ferguson, K.M.
History
DepositionJan 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Dec 25, 2019Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_genus ..._entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_genus / _entity_src_gen.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell / _entity_src_gen.pdbx_host_org_cell_line / _software.version
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Matuzumab Fab Light chain
H: Matuzumab Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5164
Polymers47,3232
Non-polymers1922
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-44 kcal/mol
Surface area18360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.821, 61.377, 102.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody Matuzumab Fab Light chain


Mass: 23235.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human/mouse chimeric derivative of mouse monoclonal antibody 425
Source: (gene. exp.) Mus musculus (house mouse) / Species: , / Strain: , / Description: humanized mouse / Cell line (production host): MYELOMA / Production host: Mus musculus (house mouse)
#2: Antibody Matuzumab Fab Heavy chain


Mass: 24087.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Human/mouse chimeric derivative of mouse monoclonal antibody 425
Source: (gene. exp.) Mus musculus (house mouse) / Species: , / Strain: , / Description: humanized mouse / Cell line (production host): MYELOMA / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 1.8M ammonium sulfate, 0.1M MES, pH 6.5, vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.15→52.7 Å / Num. all: 20191 / Num. obs: 20191 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Χ2: 1.361 / Net I/σ(I): 7.2
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 3.618 / Num. unique all: 1971 / Rsym value: 0.417 / Χ2: 0.931 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.72 Å
Translation2.5 Å49.72 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 20127
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.63-10025.80.18504
6.02-7.6330.30.72502
5.22-6.0222.40.814508
4.72-5.22210.853504
4.38-4.7219.40.897504
4.1-4.3819.20.882543
3.86-4.118.70.895566
3.67-3.8621.80.866598
3.5-3.6720.90.877632
3.35-3.522.50.855646
3.22-3.3520.60.866672
3.1-3.2224.30.852714
3-3.124.80.847717
2.9-328.30.823763
2.82-2.925.30.83764
2.74-2.82280.814801
2.66-2.7428.70.818812
2.6-2.6628.20.827831
2.53-2.627.60.804861
2.48-2.5327.50.811870
2.42-2.4829.40.797897
2.37-2.4227.40.816907
2.32-2.3732.20.791928
2.28-2.3229.70.8943
2.24-2.2829.90.795991
2.2-2.2436.80.739957
2.15-2.233.60.7321192

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DM6phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB id 1L7I

1l7i


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.897 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.362 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1029 5.1 %RANDOM
Rwork0.224 ---
all0.226 20127 --
obs0.226 20127 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.434 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2--1.35 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3097 0 10 99 3206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213233
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9524430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.2775423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50224.425113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00715442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.367157
X-RAY DIFFRACTIONr_chiral_restr0.1070.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022425
X-RAY DIFFRACTIONr_nbd_refined0.2220.21264
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22155
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2139
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.29
X-RAY DIFFRACTIONr_mcbond_it0.8321.52124
X-RAY DIFFRACTIONr_mcangle_it1.29723397
X-RAY DIFFRACTIONr_scbond_it1.1931109
X-RAY DIFFRACTIONr_scangle_it1.8854.51033
LS refinement shellResolution: 2.145→2.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 66 -
Rwork0.243 1275 -
all-1341 -
obs--90.85 %

+
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