[English] 日本語
Yorodumi
- PDB-1lhz: Structure of a Human Bence-Jones Dimer Crystallized in U.S. Space... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lhz
TitleStructure of a Human Bence-Jones Dimer Crystallized in U.S. Space Shuttle Mission STS-95: 293K
ComponentsIMMUNOGLOBULIN LAMBDA LIGHT CHAIN
KeywordsIMMUNE SYSTEM / Human Bence-Jones Dimer / Microgravity Crystallization / Induced fit
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / : / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...Immunoglobulin V-Type / Immunoglobulin V-set domain / : / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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: 2.3 Å
AuthorsTerzyan, S.S. / DeWitt, C.R. / Ramsland, P.A. / Bourne, P.C. / Edmundson, A.B.
Citation
Journal: J.MOL.RECOG. / Year: 2003
Title: Comparison of the three-dimensional structures of a human Bence-Jones dimer crystallized on Earth and aboard US Space Shuttle Mission STS-95
Authors: Terzyan, S.S. / DeWitt, C.R. / Ramsland, P.A. / Bourne, P.C. / Edmundson, A.B.
#1: Journal: 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. / Terzyans, S.S. / Moomaw, C.R. / Slaughter, C.A. / Guddat, L.W. / Edmundson, A.B.
History
DepositionApr 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Advisory / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / 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 2.1Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999sequence an appropriate sequence database reference was not available at the time of processing.

-
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
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-18 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.940, 85.170, 114.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
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*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.63 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 279 K / Method: vapor diffusion / Details: PEG 8000, VAPOR DIFFUSION, temperature 279K
Crystal grow
*PLUS
Method: unknown
Details: Alvarado, U.R., (2001) J. Crystal Growth, 223, 407.

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 19, 1998 / Details: Osmic multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 21524 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 7.6 / Num. unique all: 1943 / % possible all: 91.7
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 21254 / Num. measured all: 92994
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 91.7 % / Redundancy: 3 % / Num. unique obs: 1943 / Rmerge(I) obs: 0.161

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JVK

1jvk


Resolution: 2.3→25 Å / Cross valid method: R free / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood target for amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2116 9.7 %Random
Rwork0.173 ---
all-21254 --
obs-21237 97.2 %-
Solvent computationBsol: 40.28 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 34.85 Å2
Baniso -1Baniso -2Baniso -3
1-6.21 Å2--
2---4.735 Å2-
3----1.477 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 0 168 3322
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.13
X-RAY DIFFRACTIONc_angle_deg1.78
X-RAY DIFFRACTIONc_mcbond_it1.91.5
X-RAY DIFFRACTIONc_mcangle_it2.72
X-RAY DIFFRACTIONc_scbond_it3.22
X-RAY DIFFRACTIONc_scangle_it3.92.5
Refinement
*PLUS
Highest resolution: 2.3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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://pdbjlvh1.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