[English] 日本語
Yorodumi
- PDB-1jvk: THREE-DIMENSIONAL STRUCTURE OF AN IMMUNOGLOBULIN LIGHT CHAIN DIME... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jvk
TitleTHREE-DIMENSIONAL STRUCTURE OF AN IMMUNOGLOBULIN LIGHT CHAIN DIMER ACTING AS A LETHAL AMYLOID PRECURSOR
ComponentsIMMUNOGLOBULIN LAMBDA LIGHT CHAIN
KeywordsIMMUNE SYSTEM / Immunoglobulin light chain dimer / amyloidogenic
Function / homology
Function and homology information


extracellular region
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 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
Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsBourne, P.C. / Ramsland, P.A. / Shan, L. / Fan, Z.-C. / DeWitt, C.R. / Shultz, B.B. / Terzyan, S.S. / Edmundson, A.B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Three-dimensional structure of an immunoglobulin light-chain dimer with amyloidogenic properties.
Authors: Bourne, P.C. / Ramsland, P.A. / Shan, L. / Fan, Z.C. / DeWitt, C.R. / Shultz, B.B. / Terzyan, S.S. / Moomaw, C.R. / Slaughter, C.A. / Guddat, L.W. / Edmundson, A.B.
History
DepositionAug 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IMMUNOGLOBULIN LAMBDA LIGHT CHAIN
B: IMMUNOGLOBULIN LAMBDA LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)45,2182
Polymers45,2182
Non-polymers00
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-16 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.280, 83.320, 112.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

-
Components

#1: Antibody IMMUNOGLOBULIN LAMBDA LIGHT CHAIN / IG A L / IMMUNOGLOBULIN LAMBDA-CHAIN / IG A1 BUR


Mass: 22608.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6PJG0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.5 Å3/Da / Density % sol: 50.85 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 8, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→19.8 Å / Num. all: 32131 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 30.46 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.6
Reflection shellResolution: 1.94→2.01 Å / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3.78 / % possible all: 89.1
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 98.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 89.1 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→19.8 Å / Cor.coef. Fo:Fc: 0.934 / SU B: 5.2 / SU ML: 0.1 / SU Rfree: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25409 1717 5.1 %RANDOM
Rwork0.22137 ---
all0.223 33848 --
obs0.22309 32131 100 %-
Displacement parametersBiso mean: 30.188 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---0.15 Å20 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.94→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 0 251 3418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONp_bond_d0.0203245
X-RAY DIFFRACTIONp_angle_d1.9421.94430
X-RAY DIFFRACTIONp_chiral_restr0.1160.2508
X-RAY DIFFRACTIONp_planar_d0.00803629
X-RAY DIFFRACTIONp_plane_restr0.00803629
X-RAY DIFFRACTIONp_hb_or_metal_coord0.2460.3630
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2460.3630
X-RAY DIFFRACTIONp_xyhbond_nbd0.20.5371
X-RAY DIFFRACTIONp_mcbond_it1.2781.52149
X-RAY DIFFRACTIONp_mcangle_it2.25423475
X-RAY DIFFRACTIONp_scbond_it2.89431096
X-RAY DIFFRACTIONp_scangle_it4.434.5955
LS refinement shellHighest resolution: 1.94 Å / Rfactor Rfree: 0.326 / Rfactor Rwork: 0.276 / Total num. of bins used: 20
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.223 / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.731.9

+
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