[English] 日本語
Yorodumi
- PDB-1flr: 4-4-20 FAB FRAGMENT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1flr
Title4-4-20 FAB FRAGMENT
Components(4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT) x 2
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment ...positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / IgG immunoglobulin complex / endosome to lysosome transport / positive regulation of endocytosis / antigen processing and presentation / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / multivesicular body / complement activation, classical pathway / antigen binding / response to bacterium / positive regulation of immune response / antibacterial humoral response / extracellular space / plasma membrane / cytosol
Similarity search - Function
Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / : / Ig gamma-2A chain C region, membrane-bound form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsWhitlow, M.
Citation
Journal: Protein Eng. / Year: 1995
Title: 1.85 A structure of anti-fluorescein 4-4-20 Fab.
Authors: Whitlow, M. / Howard, A.J. / Wood, J.F. / Voss Jr., E.W. / Hardman, K.D.
#1: Journal: Proteins / Year: 1989
Title: Three-Dimensional Structure of a Fluorescein-Fab Complex Crystallized in 2-Methyl-2,4-Pentanediol
Authors: Herron, J.N. / He, X. / Mason, M.L. / Voss Junior, E.W. / Edmundson, A.B.
#2: Journal: Proteins / Year: 1988
Title: Differences in Crystal Properties and Ligand Affinities of an Antifluorescyl Fab (4-4-20) in Two Solvent Systems
Authors: Gibson, A.L. / Herron, J.N. / He, X.-M. / Patrick, V.A. / Mason, M.L. / Lin, J.-N. / Kranz, D.M. / Voss Junior, E.W. / Edmundson, A.B.
#3: Journal: J.Biol.Chem. / Year: 1989
Title: Comparison of Variable Region Primary Structures within an Anti-Fluorescein Idiotype Family
Authors: Bedzyk, W.D. / Johnson, L.S. / Riordon, G.S. / Voss, E.W.
History
DepositionJan 19, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: 4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT
H: 4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4803
Polymers48,1482
Non-polymers3321
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-27 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.750, 43.870, 58.170
Angle α, β, γ (deg.)95.15, 86.85, 98.01
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 100 / 3: CIS PROLINE - PRO L 146 / 4: CIS PROLINE - PRO H 152 / 5: CIS PROLINE - PRO H 194 / 6: WATER MOLECULE 870 IS DISORDERED.

-
Components

#1: Antibody 4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT


Mass: 24173.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: LYMPHOCYTE-PLASMA CELL / Cell line: 4-4-20 MURINE-MURINE HYBRIDOMA / Organ: SPLEEN / Variant: BALB/CV / Strain: BALB/C / References: GenBank: 1589925
#2: Antibody 4-4-20 (IG*G2A=KAPPA=) FAB FRAGMENT


Mass: 23973.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: LYMPHOCYTE-PLASMA CELL / Cell line: 4-4-20 MURINE-MURINE HYBRIDOMA / Organ: SPLEEN / Variant: BALB/CV / Strain: BALB/C / References: UniProt: P01865
#3: Chemical ChemComp-FLU / 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / FLUORESCEIN / Fluorescein


Mass: 332.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H12O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: unknown
Details: Gibson, A.L., (1988) Proteins: Struct.,Funct., Genet., 3, 155.
PH range low: 7.3 / PH range high: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMsodium phosphate11
214-30 mg/mlprotein11
325-50 %(w/v)PEG335012

-
Data collection

Diffraction sourceWavelength: 1.54
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Oct 21, 1988
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNum. obs: 29963 / % possible obs: 70 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.041
Reflection
*PLUS
Highest resolution: 1.79 Å / Num. measured all: 76616 / Rmerge(I) obs: 0.041

-
Processing

Software
NameClassification
XENGENdata collection
PROFFTrefinement
XENGENdata reduction
RefinementResolution: 1.85→10 Å / σ(F): 2
Details: RESIDUES CYS H 133 TO GLY H 138 ARE IN WEAK ELECTRON DENSITY. THERE IS A DISCONTINUITY IN THE ELECTION DENSITY MAP BETWEEN RESIDUES VAL H 132 AND CYS H 133. THE RESULTING COORDINATES, AS ...Details: RESIDUES CYS H 133 TO GLY H 138 ARE IN WEAK ELECTRON DENSITY. THERE IS A DISCONTINUITY IN THE ELECTION DENSITY MAP BETWEEN RESIDUES VAL H 132 AND CYS H 133. THE RESULTING COORDINATES, AS PRESENTED IN THIS ENTRY, CONTAIN TWO POSITIONS FOR N CYS H 133, ONE OF WHICH IS PROPERLY CONNECTED TO C VAL H 132 BUT QUITE DISTANT (5.58 ANGSTROMS) FROM CA CYS H 133. THE OTHER POSITION FOR N CYS H 133 IS PROPERLY CONNECTED TO CA H 133 BUT QUITE DISTANT (4.51 ANGSTROMS) FROM C VAL H 132.
RfactorNum. reflection
obs0.188 26328
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 25 290 3665
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.015
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it16.8711
X-RAY DIFFRACTIONp_mcangle_it17.1071.5
X-RAY DIFFRACTIONp_scbond_it19.1441.5
X-RAY DIFFRACTIONp_scangle_it20.5062
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1910.15
X-RAY DIFFRACTIONp_singtor_nbd0.1910.5
X-RAY DIFFRACTIONp_multtor_nbd0.2710.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3050.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor21.415
X-RAY DIFFRACTIONp_orthonormal_tor26.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

+
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