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BMRB: 19798

2MKW

Solution Structure of 6aJL2-R24G Amyloidogenic Light Chain Protein

Authors

Maya, R.C., Gil, P.C., Amero, C.

Assembly

6aJL2-R24G Amyloidogenic Light Chain Protein

Entity

1. 6aJL2-R24G Amyloidogenic Light Chain Protein (polymer, Thiol state: all disulfide bound), 111 monomers, 11853.70 Da Detail

NFMLTQPHSV SESPGKTVTI SCTGSSGSIA SNYVQWYQQR PGSSPTTVIY EDNQRPSGVP DRFSGSIDSS SNSASLTISG LKTEDEADYY CQSYDSSNHV VFGGGTKLTV L

Formula weight

11853.7 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS22:SG	1:CYS91:SG

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 93.3 %, Completeness (bb): 98.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.3 % (1117 of 1197)	96.7 % (594 of 614)	88.0 % (410 of 466)	96.6 % (113 of 117)
Backbone	98.0 % (641 of 654)	97.3 % (220 of 226)	98.8 % (319 of 323)	97.1 % (102 of 105)
Sidechain	89.3 % (575 of 644)	96.4 % (374 of 388)	77.9 % (190 of 244)	91.7 % (11 of 12)
Aromatic	56.1 % (55 of 98)	98.0 % (48 of 49)	12.5 % (6 of 48)	100.0 % (1 of 1)
Methyl	100.0 % (98 of 98)	100.0 % (49 of 49)	100.0 % (49 of 49)

1. entity

NFMLTQPHSV SESPGKTVTI SCTGSSGSIA SNYVQWYQQR PGSSPTTVIY EDNQRPSGVP DRFSGSIDSS SNSASLTISG LKTEDEADYY CQSYDSSNHV VFGGGTKLTV L

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]	protein	0.8 ~ 1.2 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	75 mM
4	H2O		solvent	95 %
5	D2O		solvent	5 %

LACS Plot; CA

Referencing offset: 0.14 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.14 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.08 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.72 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MKW, Strand ID: A Detail

Release date

2014-06-15

Citation

Solution structure of 6aJL2 and 6aJL2-R24G amyloidogenics light chain proteins
Maya, R.C., Gil, P.C., Amero, C.
Biochem. Biophys. Res. Commun. (2015), 456, 695-699, PubMed 25522882 , DOI 10.1016/j.bbrc.2014.12.044 , Abstract

Related entities 1. 6aJL2-R24G Amyloidogenic Light Chain Protein, : 1 : 2 : 3 : 5 : 371 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]	protein	0.8 ~ 1.2 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	75 mM
4	H2O		solvent	95 %
5	D2O		solvent	5 %

2 3D HNCACB

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]	protein	0.8 ~ 1.2 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	75 mM
4	H2O		solvent	95 %
5	D2O		solvent	5 %

3 3D 1H-13C NOESY

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]	protein	0.8 ~ 1.2 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	75 mM
4	H2O		solvent	95 %
5	D2O		solvent	5 %

4 3D 1H-15N NOESY

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]	protein	0.8 ~ 1.2 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	75 mM
4	H2O		solvent	95 %
5	D2O		solvent	5 %

5 3D 1H-15N TOCSY

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]	protein	0.8 ~ 1.2 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	75 mM
4	H2O		solvent	95 %
5	D2O		solvent	5 %

6 3D HNCA

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]	protein	0.8 ~ 1.2 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	75 mM
4	H2O		solvent	95 %
5	D2O		solvent	5 %

7 3D HNCO

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]	protein	0.8 ~ 1.2 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	75 mM
4	H2O		solvent	95 %
5	D2O		solvent	5 %

8 3D HN(CO)CA

Instrument

Varian Uniform NMR System - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-100% 13C; U-100% 15N]	protein	0.8 ~ 1.2 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium chloride	natural abundance	salt	75 mM
4	H2O		solvent	95 %
5	D2O		solvent	5 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19798_2mkw.nef
Input source #2: Coordindates	2mkw.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:22:CYS:SG	A:91:CYS:SG	oxidized, CA 55.278, CB 46.167 ppm	oxidized, CA 52.689, CB 44.837 ppm	2.036

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
NFMLTQPHSVSESPGKTVTISCTGSSGSIASNYVQWYQQRPGSSPTTVIYEDNQRPSGVPDRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSNHV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NFMLTQPHSVSESPGKTVTISCTGSSGSIASNYVQWYQQRPGSSPTTVIYEDNQRPSGVPDRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSNHV

-------110-
VFGGGTKLTVL
|||||||||||
VFGGGTKLTVL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	111	0	0	100.0

Content subtype: combined_19798_2mkw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	1073		97.3 (chain: A, length: 111)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	1489 (1)	noe	99.1 (chain: A, length: 111)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	1 (1)	undefined	1.8 (chain: A, length: 111)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	62 (1)	hbond	33.3 (chain: A, length: 111)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	194 (194)	.	98.2 (chain: A, length: 111)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 97.3%
- Total number of assignments
  - ¹H chemical shifts: 577
  - ¹⁵N chemical shifts: 104
  - ¹³C chemical shifts: 392
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 99.1%
- Total number of restraints: 1482
- Weight of restraints: 1.0 (1482)
- Potential type of restraints: square-well-parabolic (1482)
- Range of distance target values: 2.95, 3.88 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 1.8%
  - Total number of restraints: 1
  - Weight of restraints: 1.0 (1)
  - Potential type of restraints: square-well-parabolic (1)
  - Range of distance target values: 2.02, 2.02 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 33.3%
    - Total number of restraints: 62
    - Weight of restraints: 1.0 (62)
    - Potential type of restraints: square-well-parabolic (62)
    - Range of distance target values: 1.9, 2.85 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 98.2%
- Total number of restraints: 194
- Total number of restraints per polymer type: 194
- Weight of restraints: 1.0 (194)
- Potential type of restraints: square-well-parabolic (194)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords AL, Amyloidosis, Germ line, lambda 6, Light chain, R24G