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- PDB-6l98: Crystalline cast nephropathy-causing Bence-Jones protein AK: An e... -

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Basic information

Entry
Database: PDB / ID: 6l98
TitleCrystalline cast nephropathy-causing Bence-Jones protein AK: An entire immunoglobulin lambda light chain dimer
ComponentsBence-Jones protein lambda light chain AK
KeywordsIMMUNE SYSTEM / Bence-Jones protein / immunoglobulin / lambda light chain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsNakagaki, T. / Noguchi, K. / Yohda, M. / Odaka, M. / Wakui, H. / Matsumura, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science19K17728 Japan
CitationJournal: Kidney Int Rep / Year: 2020
Title: Multiple Myeloma-Associated Ig Light Chain Crystalline Cast Nephropathy.
Authors: 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. / ...Authors: 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.
History
DepositionNov 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bence-Jones protein lambda light chain AK
B: Bence-Jones protein lambda light chain AK


Theoretical massNumber of molelcules
Total (without water)45,2802
Polymers45,2802
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-19 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.379, 71.794, 98.455
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody Bence-Jones protein lambda light chain AK


Mass: 22639.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM MES 15% glycerol 15% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2019
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 42953 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 29.82 Å2 / CC1/2: 0.596 / Net I/σ(I): 18.8
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 6.7 % / Num. unique obs: 4233 / CC1/2: 0.596 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HK0

4hk0


Resolution: 1.77→33.86 Å / SU ML: 0.2415 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.7699
RfactorNum. reflection% reflection
Rfree0.2651 2102 4.9 %
Rwork0.2291 --
obs0.2308 42885 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.02 Å2
Refinement stepCycle: LAST / Resolution: 1.77→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 0 109 3272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713243
X-RAY DIFFRACTIONf_angle_d0.91244434
X-RAY DIFFRACTIONf_chiral_restr0.0578499
X-RAY DIFFRACTIONf_plane_restr0.006580
X-RAY DIFFRACTIONf_dihedral_angle_d6.7751942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.35421260.31092634X-RAY DIFFRACTION96.91
1.81-1.860.33051430.2982667X-RAY DIFFRACTION100
1.86-1.910.33891340.28822676X-RAY DIFFRACTION99.93
1.91-1.960.29041590.27112688X-RAY DIFFRACTION100
1.96-2.030.33121380.27212694X-RAY DIFFRACTION100
2.03-2.10.32091310.26612711X-RAY DIFFRACTION100
2.1-2.180.32781310.26372696X-RAY DIFFRACTION100
2.18-2.280.2931520.25932689X-RAY DIFFRACTION100
2.28-2.40.28791500.25592703X-RAY DIFFRACTION99.76
2.4-2.560.28651180.26312728X-RAY DIFFRACTION99.82
2.56-2.750.34191380.26172732X-RAY DIFFRACTION100
2.75-3.030.29191440.26382736X-RAY DIFFRACTION99.9
3.03-3.470.24811270.24132760X-RAY DIFFRACTION100
3.47-4.370.25771500.19662775X-RAY DIFFRACTION99.63
4.37-33.860.19181610.16922894X-RAY DIFFRACTION99.64

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