[English] 日本語
Yorodumi
- PDB-1bjm: LOC NAKS, A LAMBDA 1 TYPE LIGHT-CHAIN DIMER (BENCE-JONES PROTEIN)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bjm
TitleLOC NAKS, A LAMBDA 1 TYPE LIGHT-CHAIN DIMER (BENCE-JONES PROTEIN) CRYSTALLIZED IN NAKSO4
ComponentsLOC - LAMBDA 1 TYPE LIGHT-CHAIN DIMER
KeywordsIMMUNOGLOBULIN / BENCE JONES / ANTIBODY / MULTIPLE QUATERNARY STRUCTURES
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSchiffer, M. / Huang, D.B.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Three quaternary structures for a single protein.
Authors: Huang, D.B. / Ainsworth, C.F. / Stevens, F.J. / Schiffer, M.
#1: Journal: Biochemistry / Year: 1985
Title: Novel Arrangement of Immunoglobulin Variable Domains: X-Ray Crystallographic Analysis of the Lambda-Chain Dimer Bence-Jones Protein Loc
Authors: Chang, C.-H. / Short, M.T. / Westholm, F.A. / Stevens, F.J. / Wang, B.-C. / Furey Junior, W. / Solomon, A. / Schiffer, M.
History
DepositionMay 26, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LOC - LAMBDA 1 TYPE LIGHT-CHAIN DIMER
B: LOC - LAMBDA 1 TYPE LIGHT-CHAIN DIMER


Theoretical massNumber of molelcules
Total (without water)45,5402
Polymers45,5402
Non-polymers00
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-24 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.870, 72.620, 63.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 145 / 2: CIS PROLINE - PRO B 145

-
Components

#1: Antibody LOC - LAMBDA 1 TYPE LIGHT-CHAIN DIMER / BENCE-JONES PROTEIN


Mass: 22769.982 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CRYSTALLIZED IN NA/K SO4 / Source: (natural) Homo sapiens (human) / References: PIR: S25754
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal grow
*PLUS
pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.95 Mammonium sulfate11
20.4 M11K2SO4
30.04 Mphosphate11

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→25.6 Å / Num. obs: 18459

-
Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→10 Å / σ(F): 3 /
RfactorNum. reflection% reflection
obs0.158 14084 76.3 %
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 0 298 3494
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0430.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0570.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8891
X-RAY DIFFRACTIONp_mcangle_it1.5981.5
X-RAY DIFFRACTIONp_scbond_it1.181.5
X-RAY DIFFRACTIONp_scangle_it1.9132
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1930.15
X-RAY DIFFRACTIONp_singtor_nbd0.2190.5
X-RAY DIFFRACTIONp_multtor_nbd0.3130.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3070.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor25.413
X-RAY DIFFRACTIONp_orthonormal_tor18.920
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