[English] 日本語
Yorodumi
- PDB-2orb: The structure of the anti-c-myc antibody 9E10 Fab fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2orb
TitleThe structure of the anti-c-myc antibody 9E10 Fab fragment
Components(Monoclonal anti-c-myc antibody 9E10) x 2
KeywordsIMMUNE SYSTEM / ANTIGEN-ANTIBODY COMPLEX / ANTIGEN RECOGNITION / long CDR H3
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKrauss, N. / Scheerer, P. / Hoehne, W.
CitationJournal: Proteins / Year: 2008
Title: The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex reveals a novel binding mode dominated by the heavy chain hypervariable loops.
Authors: Krauss, N. / Wessner, H. / Welfle, K. / Welfle, H. / Scholz, C. / Seifert, M. / Zubow, K. / Ay, J. / Hahn, M. / Scheerer, P. / Skerra, A. / Hohne, W.
History
DepositionFeb 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Monoclonal anti-c-myc antibody 9E10
H: Monoclonal anti-c-myc antibody 9E10
M: Monoclonal anti-c-myc antibody 9E10
I: Monoclonal anti-c-myc antibody 9E10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9956
Polymers97,8034
Non-polymers1922
Water4,630257
1
L: Monoclonal anti-c-myc antibody 9E10
H: Monoclonal anti-c-myc antibody 9E10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0934
Polymers48,9012
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-42 kcal/mol
Surface area18950 Å2
MethodPISA, PQS
2
M: Monoclonal anti-c-myc antibody 9E10
I: Monoclonal anti-c-myc antibody 9E10


Theoretical massNumber of molelcules
Total (without water)48,9012
Polymers48,9012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-34 kcal/mol
Surface area19090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.593, 65.462, 117.689
Angle α, β, γ (deg.)90.00, 96.97, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody Monoclonal anti-c-myc antibody 9E10


Mass: 24001.543 Da / Num. of mol.: 2 / Fragment: light chain of antigen binding fragment, Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#2: Antibody Monoclonal anti-c-myc antibody 9E10


Mass: 24899.799 Da / Num. of mol.: 2 / Fragment: heavy chain of antigen binding fragment, Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#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.: 257 / 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: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.05
Details: 15% PEG 3350, 0.2M ammonium sulfate, 0.1 M sodium citrate buffer, pH 3.05, 0.02% sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 25, 2004
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 37773 / Num. obs: 37773 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 41.2 Å2 / Rsym value: 0.046 / Net I/σ(I): 19.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1278 / Rsym value: 0.345 / % possible all: 62.1

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OR9

2or9


Resolution: 2.2→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.317 1938 -RANDOM
Rwork0.261 ---
all-37692 --
obs-37692 91.3 %-
Displacement parametersBiso mean: 46.8 Å2
Baniso -1Baniso -2Baniso -3
1-10 Å20 Å21.8 Å2
2---19.7 Å20 Å2
3---9.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6464 0 10 257 6731
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_deg27.08
X-RAY DIFFRACTIONc_improper_angle_deg0.924
LS refinement shellResolution: 2.2→2.28 Å
RfactorNum. reflection% reflection
Rfree0.46 149 -
Rwork0.376 --
obs-2856 70 %

+
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