[English] 日本語
Yorodumi
- PDB-1m71: Crystal structure of a Monoclonal Fab Specific for Shigella Flexn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m71
TitleCrystal structure of a Monoclonal Fab Specific for Shigella Flexneri Y lipopolysaccharide
Components
  • heavy chain of the monoclonal antibody Fab SYA/J6
  • light chain of the monoclonal antibody Fab SYA/J6
KeywordsIMMUNE SYSTEM / Fab-carbohydrate interactions / anti-carbohydrate antibody / X-ray Diffracrion / Shigella O-antigen
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / metal ion binding
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
If kappa light chain / Ig heavy chain V-III region J606
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVyas, N.K. / Vyas, M.N. / Chervenak, M.C. / Johnson, M.A. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A.
Citation
Journal: Biochemistry / Year: 2002
Title: Molecular Recognition of Oligosaccharide Epitopes by a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide: X-ray Structures and Thermodyanamics
Authors: Vyas, N.K. / Vyas, M.N. / Chervenak, M.C. / Johnson, M.A. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Preliminary Crystallographic Analysis of a Fab Specific for the O-antigen of Shigella flexneri Cell Surface Lipopolysaccharide with and without Bound Saccharides
Authors: Vyas, N.K. / Vyas, M.N. / Meikkle, P.J. / Sinnott, B. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A.
History
DepositionJul 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE AT THE TIME OF PROCESSING, THIS SEQUENCE OF CHAIN A AND CHAIN B HAVE NOT YET BEEN ...SEQUENCE AT THE TIME OF PROCESSING, THIS SEQUENCE OF CHAIN A AND CHAIN B HAVE NOT YET BEEN DEPOSITED IN A SEQUENCE DATABASE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: light chain of the monoclonal antibody Fab SYA/J6
B: heavy chain of the monoclonal antibody Fab SYA/J6


Theoretical massNumber of molelcules
Total (without water)47,2652
Polymers47,2652
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-22 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.700, 70.700, 202.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Antibody light chain of the monoclonal antibody Fab SYA/J6


Mass: 23717.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/C / Cell: Plasmacytoma cell / Cell line: SYA/J6 hybridoma / Organ: Spleen / Production host: Escherichia coli (E. coli) / References: UniProt: A2NHM3*PLUS
#2: Antibody heavy chain of the monoclonal antibody Fab SYA/J6


Mass: 23547.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/C / Cell: Plasmacytoma cell / Cell line: SYA/J6 hybridoma / Organ: Spleen / Production host: Escherichia coli (E. coli) / References: UniProt: P01801*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.52 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: MPD, potassium phosphate, pH 6.5, VAPOR DIFFUSION, temperature 277K
Crystal grow
*PLUS
Details: Vyas, M.N., (1993) J. Mol. Biol., 231, 133.

-
Data collection

DiffractionMean temperature: 281 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 2, 1990
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 10392 / % possible obs: 77.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 6 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.08 / Net I/σ(I): 5
Reflection shellResolution: 2.8→2.97 Å / Num. unique all: 1236 / % possible all: 59.9
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 108812
Reflection shell
*PLUS
% possible obs: 59.9 %

-
Processing

Software
NameVersionClassification
Weissenbergdata collection
WEISdata reduction
MERLOTphasing
CNS1refinement
WEISSENBERGdata reduction
WEISdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MPC

1mpc


Resolution: 2.8→19.76 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 38035.32 / Data cutoff high rms absF: 38035.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.5 / Stereochemistry target values: Engh & Huber
Details: Author states residues 127-135 of chain B is part of a disordered segment, Bulk Solvent Model Used.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 551 5.3 %RANDOM
Rwork0.223 ---
all-10392 --
obs-10392 77.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.201803 e/Å3
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.55 Å20 Å20 Å2
2--5.55 Å20 Å2
3----11.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.79 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 0 62 3385
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it0.841.5
X-RAY DIFFRACTIONc_mcangle_it1.382
X-RAY DIFFRACTIONc_scbond_it0.512
X-RAY DIFFRACTIONc_scangle_it0.932.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.41 67 5.1 %
Rwork0.375 1236 -
obs--59.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.292
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
LS refinement shell
*PLUS
Rfactor Rfree: 0.41

+
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