[English] 日本語
Yorodumi
- PDB-1f90: FAB FRAGMENT OF MONOCLONAL ANTIBODY (LNKB-2) AGAINST HUMAN INTERL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f90
TitleFAB FRAGMENT OF MONOCLONAL ANTIBODY (LNKB-2) AGAINST HUMAN INTERLEUKIN-2 IN COMPLEX WITH ANTIGENIC PEPTIDE
Components
  • (FAB FRAGMENT OF MONOCLONAL ANTIBODY) x 2
  • ANTIGENIC NONAPEPTIDE
KeywordsIMMUNE SYSTEM / monoclonal antibody / antigen-binding fragment / interleukin-2 / antigenic peptide
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsAfonin, P.V. / Fokin, A.V. / Tsigannik, I.N. / Mikhailova, I.Y. / Onoprienko, L.V. / Mikhaleva, I.I. / Ivanov, V.T. / Mareeva, T.Y. / Nesmeyanov, V.A. / Li, N. ...Afonin, P.V. / Fokin, A.V. / Tsigannik, I.N. / Mikhailova, I.Y. / Onoprienko, L.V. / Mikhaleva, I.I. / Ivanov, V.T. / Mareeva, T.Y. / Nesmeyanov, V.A. / Li, N. / Duax, W.L. / Pletnev, V.Z.
Citation
Journal: Protein Sci. / Year: 2001
Title: Crystal structure of an anti-interleukin-2 monoclonal antibody Fab complexed with an antigenic nonapeptide.
Authors: Afonin, P.V. / Fokin, A.V. / Tsygannik, I.N. / Mikhailova, I.Y. / Onoprienko, L.V. / Mikhaleva, I.I. / Ivanov, V.T. / Mareeva, T.Y. / Nesmeyanov, V.A. / Li, N. / Pangborn, W.A. / Duax, W.L. / Pletnev, V.Z.
#1: Journal: BIOORG.KHIM. / Year: 2000
Title: THREE-DIMENSIONAL STRUCTURE OF ANTIGEN BINDING FRAGMENT OF MONOCLONAL ANTIBODY AGAINST HUMAN INTERLEUKIN-2 IN TWO CRYSTAL FORMS AT 2.2 AND 2.9 A RESOLUTION.
Authors: Fokin, A.V. / Afonin, P.V. / Mikhailova, I.Y. / Tsygannik, I.N. / Mareeva, T.Y. / Nesmeyanov, V.A. / Pangborn, W. / Lee, N. / Duax, W. / Sijak, E. / Pletnev, V.Z.
History
DepositionJul 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Remark 999SEQUENCE The sequence of the protein has not been deposited in any sequence database. It was ...SEQUENCE The sequence of the protein has not been deposited in any sequence database. It was published in the Bioorganicheskaya Khimiya (Rus) (1995), V21, N6, p430-435. "Cloning cDNA Encoding Fv-Fragments of the Light and Heavy Chains of the Monoclonal Antibody" by A.I.Paskhin, T.N. Golovina, V.A. Nesmeyanov, V.G. Korobko.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: FAB FRAGMENT OF MONOCLONAL ANTIBODY
H: FAB FRAGMENT OF MONOCLONAL ANTIBODY
E: ANTIGENIC NONAPEPTIDE


Theoretical massNumber of molelcules
Total (without water)49,1133
Polymers49,1133
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-27 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.83, 72.76, 72.15
Angle α, β, γ (deg.)90.0, 106.98, 90.0
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody FAB FRAGMENT OF MONOCLONAL ANTIBODY


Mass: 24203.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA
#2: Antibody FAB FRAGMENT OF MONOCLONAL ANTIBODY


Mass: 23853.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA
#3: Protein/peptide ANTIGENIC NONAPEPTIDE


Mass: 1055.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The Peptide was Chemically Synthetized in Solution
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG-4000, 2-propanol, Na-citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-7 mg/mlprotein1drop
212-13 %PEG40001reservoir
312-13 %2-propanol1reservoir
460 mMsodium citrate1reservoir

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→99 Å / Num. all: 13733 / Num. obs: 11984 / % possible obs: 83.4 % / Observed criterion σ(F): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 6.9
Reflection shellResolution: 2.6→2.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5825 / Num. unique all: 1850 / % possible all: 97.15
Reflection
*PLUS
Num. obs: 9377 / % possible obs: 99.7 % / Num. measured all: 19271 / Rmerge(I) obs: 0.112

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNS0.9refinement
X-PLORphasing
RefinementResolution: 2.6→99 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Cross-validated maximum likelihood simulated annealing refinement (CNS package)
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1212 -Random
Rwork0.165 ---
all-14376 --
obs-13733 95.5 %-
Refinement stepCycle: LAST / Resolution: 2.6→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4247 0 0 267 4514
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_torsion_deg27.3
X-RAY DIFFRACTIONc_torsion_impr_deg0.85
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 99 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rfree: 0.263
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

+
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