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BMRB: 16606

2KQM

SOLUTION STRUCTURE OF THE KI O18/O8 Y87H IMMUNOGLOBULIN LIGHT CHAIN VARIABLE DOMAIN

Authors

Volkman, B.F., Peterson, F.C., Ramirez-Alvarado, M., Baden, E.M.

Assembly

kI O18/O8 Y87H

Entity

1. kI O18/O8 Y87H (polymer, Thiol state: all disulfide bound), 110 monomers, 12094.21 × 2 Da Detail

STDIQMTQSP SSLSASVGDR VTITCQASQD ISNYLNWYQQ KPGKAPKLLI YDASNLETGV PSRFSGSGSG TDFTFTISSL QPEDIATYHC QQYDNLPYTF GQGTKLEIKR

Total weight

24188.42 Da

Max. entity weight

12094.21 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS25:SG	1:CYS90:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 95.8 %, Completeness (bb): 97.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.8 % (1196 of 1249)	97.4 % (630 of 647)	93.6 % (452 of 483)	95.8 % (114 of 119)
Backbone	97.5 % (632 of 648)	98.2 % (218 of 222)	97.2 % (313 of 322)	97.1 % (101 of 104)
Sidechain	94.5 % (664 of 703)	96.9 % (412 of 425)	90.9 % (239 of 263)	86.7 % (13 of 15)
Aromatic	78.8 % (82 of 104)	98.1 % (51 of 52)	58.8 % (30 of 51)	100.0 % (1 of 1)
Methyl	97.1 % (101 of 104)	96.2 % (50 of 52)	98.1 % (51 of 52)

1. kI O18/O8 Y87H

STDIQMTQSP SSLSASVGDR VTITCQASQD ISNYLNWYQQ KPGKAPKLLI YDASNLETGV PSRFSGSGSG TDFTFTISSL QPEDIATYHC QQYDNLPYTF GQGTKLEIKR

Show sample condition

Sample

Solvent system 95% H2O, 5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.8 mM kI O18/O8 Y87H U-15N/13C, 10 mM MES

#	Name	Isotope labeling	Concentration
1	kI O18/O8 Y87H	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	[U-2H]	10 mM
3	sodium azide	natural abundance	0.02 %
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.46 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.46 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.08 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.62 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2010-05-12

Related entities 1. kI O18/O8 Y87H, : 1 : 2 : 414 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16606_2kqm.nef
Input source #2: Coordindates	2kqm.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:23:CYS:SG	A:88:CYS:SG	oxidized, CA 56.31, CB 49.592 ppm	oxidized, CA 52.512, CB 45.723 ppm	2.033
B:223:CYS:SG	B:288:CYS:SG	unknown	unknown	2.044

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

-0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------1
STDIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYHCQQYDNLPYTF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
STDIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYHCQQYDNLPYTF
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

00--------
GQGTKLEIKR
||||||||||
GQGTKLEIKR
-------110

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

-200-----210-------220-------230-------240-------250-------260-------270-------280-------290-------3
STDIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYHCQQYDNLPYTF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
STDIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYHCQQYDNLPYTF
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

00--------
GQGTKLEIKR
||||||||||
GQGTKLEIKR
-------110

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	110	0	0	100.0
B	B	110	0	0	100.0

Content subtype: combined_16606_2kqm.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1201		98.2 (chain: A, length: 110)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	6277 (1)	noe	98.2 (chain: A, length: 110), 98.2 (chain: B, length: 110)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	302 (302)	.	94.5 (chain: A, length: 110), 94.5 (chain: B, length: 110)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 98.2%
- Total number of assignments
  - ¹H chemical shifts: 635
  - ¹³C chemical shifts: 452
  - ¹⁵N chemical shifts: 114
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
86	TYR	HH	10.65
97	THR	HG1	5.176

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	647	633	97.8
¹³C chemical shifts	483	452	93.6
¹⁵N chemical shifts	122	114	93.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	222	218	98.2
¹³C chemical shifts	220	213	96.8
¹⁵N chemical shifts	104	101	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	425	415	97.6
¹³C chemical shifts	263	239	90.9
¹⁵N chemical shifts	18	13	72.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	52	98.1
¹³C chemical shifts	53	52	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	51	98.1
¹³C chemical shifts	51	30	58.8
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 98.2%
  - Entity_assembly_ID: B, Chain length: 110, Sequence coverage: 98.2%
- Total number of restraints: 6272
- Weight of restraints: 1.0 (6272)
- Potential type of restraints: upper-bound-parabolic (6272)
- Range of distance target values: 2.1, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 94.5%
  - Entity_assembly_ID: B, Chain length: 110, Sequence coverage: 94.5%
- Total number of restraints: 302
- Total number of restraints per polymer type: 302
- Weight of restraints: 1.0 (302)
- Potential type of restraints: square-well-parabolic (302)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords Amyloidosis, homodimer, Immunoglobulin kappa light chain, NMR

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Found 1 Document (0.936 seconds)

BMRB: 16606

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. kI O18/O8 Y87H, : 1 : 2 : 414 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail