6L98 | pdb_00006l98

Crystalline cast nephropathy-causing Bence-Jones protein AK: An entire immunoglobulin lambda light chain dimer

• PDB DOI: https://doi.org/10.2210/pdb6L98/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-11-08 Released: 2020-09-23 
• Deposition Author(s): Nakagaki, T., Noguchi, K., Yohda, M., Odaka, M., Wakui, H., Matsumura, H.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Multiple Myeloma-Associated Ig Light Chain Crystalline Cast Nephropathy.

Matsumura, H., Furukawa, Y., Nakagaki, T., Furutani, C., Osanai, S., Noguchi, K., Odaka, M., Yohda, M., Ohtani, H., Michishita, Y., Kawabata, Y., Kitabayashi, A., Ikeda, S., Nara, M., Komatsuda, A., Takahashi, N., Wakui, H.

(2020) Kidney Int Rep 5: 1595-1602

• DOI: https://doi.org/10.1016/j.ekir.2020.06.026

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 45.28 kDa 
• Atom Count: 3,272 
• Modelled Residue Count: 423 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bence-Jones protein lambda light chain AK	A, B	213	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.379	α = 90
b = 71.794	β = 90
c = 98.455	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-23 
Deposition Author(s): Nakagaki, T., Noguchi, K., Yohda, M., Odaka, M., Wakui, H., Matsumura, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	19K17728

Revision History  

• Version 1.0: 2020-09-23
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary