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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.265 (Depositor), 0.267 (DCC)
R-Value Work:
0.229 (Depositor), 0.230 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.265 (Depositor), 0.267 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-09-23

Deposition Author(s):

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

Revision History (Full details and data files)

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