BMRBj - BMREntryMaster

Found 1 Document (0.994 seconds)

BMRB: 16607

2KQN

SOLUTION STRUCTURE OF THE AL-09 H87Y IMMUNOGLOBULIN LIGHT CHAIN VARIABLE DOMAIN

Authors

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

Assembly

AL-09 H87Y

Entity

1. AL-09 H87Y (polymer, Thiol state: all disulfide bound), 110 monomers, 12147.31 × 2 Da Detail

STDIQMTQSP SSLSASVGDR VTITCQASQD INNYLIWYQQ KPGQAPKLLI YDASTLETGV PSRFSGSGSG TEFTFTISSL QPEDLATYYC QQYDNLPYTF GQGTKLEIKR

Total weight

24294.62 Da

Max. entity weight

12147.31 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS25:SG	1:CYS90:SG
2	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: 98.2 %, Completeness: 96.3 %, Completeness (bb): 97.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.3 % (1211 of 1257)	98.0 % (637 of 650)	93.6 % (457 of 488)	98.3 % (117 of 119)
Backbone	97.8 % (634 of 648)	98.2 % (218 of 222)	97.5 % (314 of 322)	98.1 % (102 of 104)
Sidechain	95.2 % (677 of 711)	97.9 % (419 of 428)	90.7 % (243 of 268)	100.0 % (15 of 15)
Aromatic	77.8 % (84 of 108)	96.3 % (52 of 54)	58.5 % (31 of 53)	100.0 % (1 of 1)
Methyl	98.2 % (108 of 110)	98.2 % (54 of 55)	98.2 % (54 of 55)

1. AL-09 H87Y

STDIQMTQSP SSLSASVGDR VTITCQASQD INNYLIWYQQ KPGQAPKLLI YDASTLETGV PSRFSGSGSG TEFTFTISSL QPEDLATYYC 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 AL-09 H87Y U-15N/13C, 10 mM MES

#	Name	Isotope labeling	Concentration
1	AL-09 H87Y	[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: -0.19 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: -0.19 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: -0.14 ppm, Outliers: 2 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: 0.68 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2010-05-12

Related entities 1. AL-09 H87Y, : 1 : 1 : 1 : 405 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_16607_2kqn.nef
Input source #2: Coordindates	2kqn.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 56.155, CB 49.4 ppm	oxidized, CA 52.375, CB 45.75 ppm	2.039
B:223:CYS:SG	B:288:CYS:SG	unknown	unknown	2.042

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
STDIQMTQSPSSLSASVGDRVTITCQASQDINNYLIWYQQKPGQAPKLLIYDASTLETGVPSRFSGSGSGTEFTFTISSLQPEDLATYYCQQYDNLPYTF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
STDIQMTQSPSSLSASVGDRVTITCQASQDINNYLIWYQQKPGQAPKLLIYDASTLETGVPSRFSGSGSGTEFTFTISSLQPEDLATYYCQQYDNLPYTF
--------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
STDIQMTQSPSSLSASVGDRVTITCQASQDINNYLIWYQQKPGQAPKLLIYDASTLETGVPSRFSGSGSGTEFTFTISSLQPEDLATYYCQQYDNLPYTF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
STDIQMTQSPSSLSASVGDRVTITCQASQDINNYLIWYQQKPGQAPKLLIYDASTLETGVPSRFSGSGSGTEFTFTISSLQPEDLATYYCQQYDNLPYTF
--------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_16607_2kqn.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	1204		98.2 (chain: A, length: 110)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	5208 (1)	noe	97.3 (chain: A, length: 110), 97.3 (chain: B, length: 110)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	298 (298)	.	92.7 (chain: A, length: 110), 92.7 (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: 454
  - ¹⁵N chemical shifts: 115
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
86	TYR	HH	10.619

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	650	634	97.5
¹³C chemical shifts	488	454	93.0
¹⁵N chemical shifts	122	115	94.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	222	216	97.3
¹³C chemical shifts	220	213	96.8
¹⁵N chemical shifts	104	100	96.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	428	418	97.7
¹³C chemical shifts	268	241	89.9
¹⁵N chemical shifts	18	15	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	55	98.2
¹³C chemical shifts	56	55	98.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	51	94.4
¹³C chemical shifts	53	29	54.7
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: 97.3%
  - Entity_assembly_ID: B, Chain length: 110, Sequence coverage: 97.3%
- Total number of restraints: 5202
- Weight of restraints: 1.0 (5202)
- Potential type of restraints: upper-bound-parabolic (5202)
- 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: 92.7%
  - Entity_assembly_ID: B, Chain length: 110, Sequence coverage: 92.7%
- Total number of restraints: 298
- Total number of restraints per polymer type: 298
- Weight of restraints: 1.0 (298)
- Potential type of restraints: square-well-parabolic (298)
- 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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.994 seconds)

BMRB: 16607

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. AL-09 H87Y, : 1 : 1 : 1 : 405 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail