BMRBj - BMREntryMaster

Found 1 Document (1.65 seconds)

BMRB: 30150

6BF2

Solution structure of a Bcl-xL S62E mutant

Authors

Follis, A.V., Kriwacki, R.

Assembly

Bcl-2-like protein 1

Entity

1. Bcl-2-like protein 1 (polymer), 212 monomers, 23689.78 Da Detail

GHSMSQSNRE LVVDFLSYKL SQKGYSWSQF SDVEENRTEA PEGTESEMET PSAINGNPSW HLADEPAVNG ATGHSSSLDA REVIPMAAVK QALREAGDEF ELRYRRAFSD LTSQLHITPG TAYQSFEQVV NELFRDGVNW GRIVAFFSFG GALCVESVDK EMQVLVSRIA AWMATYLNDH LEPWIQENGG WDTFVELYGN NAAAESRKGQ ER

Formula weight

23689.78 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 96.2 %, Completeness: 83.0 %, Completeness (bb): 96.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.0 % (1997 of 2405)	88.8 % (1103 of 1242)	73.0 % (680 of 931)	92.2 % (214 of 232)
Backbone	96.2 % (1210 of 1258)	96.8 % (419 of 433)	94.8 % (588 of 620)	99.0 % (203 of 205)
Sidechain	72.7 % (976 of 1343)	84.5 % (684 of 809)	55.4 % (281 of 507)	40.7 % (11 of 27)
Aromatic	50.4 % (121 of 240)	89.2 % (107 of 120)	7.0 % (8 of 114)	100.0 % (6 of 6)
Methyl	91.1 % (184 of 202)	97.0 % (98 of 101)	85.1 % (86 of 101)

1. entity 1

Show sample condition

Sample #1

Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1), Details 2.2 mM [U-99% 13C; U-99% 15N] Bcl-xL S62E, 92% H2O/8% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl-xL S62E	[U-99% 13C; U-99% 15N]		2.2 (±0.1) mM

Sample #2

Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1), Details 1.9 mM [U-99% 13C; U-99% 15N] Bcl-xL S62E, 92% H2O/8% D2O

#	Name	Isotope labeling	Type	Concentration
2	Bcl-xL S62E	[U-99% 13C; U-99% 15N]		1.9 (±0.1) mM

LACS Plot; CA

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

Referencing offset: 1.18 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 1.18 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.23 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.18 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5L1Y, Strand ID: A Detail

Release date

2016-11-10

Citation

Regulation of apoptosis by an intrinsically disordered region of Bcl-xL
Follis, A.V., Llambi, F., Kalkavan, H., Yao, Y., Phillips, A.H., Park, C.G., Marassi, F.M., Green, D.R., Kriwacki, R.W.
Nat. Chem. Biol. (2018), 14, 458-465, PubMed 29507390 , DOI 10.1038/s41589-018-0011-x , Abstract

Related entities 1. Bcl-2-like protein 1, : 1 : 14 : 91 entities Detail

Interaction partners 1. Bcl-2-like protein 1, : 87 interactors Detail

More details for 87 interactors identified by 36 citations

Experiments performed 7 experiments Detail

1 3D HNCACB

Instrument

Bruker AvanceIII - 600 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1), Details 2.2 mM [U-99% 13C; U-99% 15N] Bcl-xL S62E, 92% H2O/8% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl-xL S62E	[U-99% 13C; U-99% 15N]		2.2 (±0.1) mM

2 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz TCI cryoprobe

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bcl-xL S62E	[U-99% 13C; U-99% 15N]		2.2 (±0.1) mM

3 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz TCI cryoprobe

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bcl-xL S62E	[U-99% 13C; U-99% 15N]		2.2 (±0.1) mM

4 3D HN(CA)CO

Instrument

Bruker AvanceIII - 600 MHz TCI cryoprobe

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bcl-xL S62E	[U-99% 13C; U-99% 15N]		2.2 (±0.1) mM

5 3D 1H-15N NOESY

Instrument

Bruker AvanceII - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 (±0.01) atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1), Details 1.9 mM [U-99% 13C; U-99% 15N] Bcl-xL S62E, 92% H2O/8% D2O

#	Name	Isotope labeling	Type	Concentration
2	Bcl-xL S62E	[U-99% 13C; U-99% 15N]		1.9 (±0.1) mM

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceII - 800 MHz TCI cryoprobe

Sample

#	Name	Isotope labeling	Type	Concentration
2	Bcl-xL S62E	[U-99% 13C; U-99% 15N]		1.9 (±0.1) mM

7 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceII - 800 MHz TCI cryoprobe

Sample

#	Name	Isotope labeling	Type	Concentration
2	Bcl-xL S62E	[U-99% 13C; U-99% 15N]		1.9 (±0.1) mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30150_6bf2.nef
Input source #2: Coordindates	6bf2.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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
GHSMSQSNRELVVDFLSYKLSQKGYSWSQFSDVEENRTEAPEGTESEMETPSAINGNPSWHLADEPAVNGATGHSSSLDAREVIPMAAVKQALREAGDEF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHSMSQSNRELVVDFLSYKLSQKGYSWSQFSDVEENRTEAPEGTESEMETPSAINGNPSWHLADEPAVNGATGHSSSLDAREVIPMAAVKQALREAGDEF

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
ELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDKEMQVLVSRIAAWMATYLNDHLEPWIQENGGWDTFVELYGN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDKEMQVLVSRIAAWMATYLNDHLEPWIQENGGWDTFVELYGN

-------210--
NAAAESRKGQER
||||||||||||
NAAAESRKGQER

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	212	0	0	100.0

Content subtype: combined_30150_6bf2.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1937		95.8 (chain: A, length: 212)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	4715 (1)	noe	98.6 (chain: A, length: 212)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	134 (1)	hbond	48.1 (chain: A, length: 212)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	270 (270)	.	79.2 (chain: A, length: 212)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 212, Sequence coverage: 95.8%
- Total number of assignments
  - ¹H chemical shifts: 1081
  - ¹³C chemical shifts: 647
  - ¹⁵N chemical shifts: 209
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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)
61	HIS	HD1	8.269
74	HIS	HD1	6.722
104	TYR	HH	8.483
116	HIS	HD1	6.7
180	HIS	HD1	6.921
180	HIS	HE2	1.175

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1242	1075	86.6
¹³C chemical shifts	931	647	69.5
¹⁵N chemical shifts	244	209	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	433	419	96.8
¹³C chemical shifts	424	397	93.6
¹⁵N chemical shifts	205	203	99.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	809	656	81.1
¹³C chemical shifts	507	250	49.3
¹⁵N chemical shifts	39	6	15.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	106	100	94.3
¹³C chemical shifts	106	83	78.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	120	103	85.8
¹³C chemical shifts	114	0	0.0
¹⁵N chemical shifts	6	6	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 212, Sequence coverage: 98.6%
- Total number of restraints: 4675
- Weight of restraints: 1.0 (4675)
- Potential type of restraints: upper-bound-parabolic (4675)
- Range of distance target values: 2.79, 10.76 (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: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 212, Sequence coverage: 48.1%
  - Total number of restraints: 134
  - Weight of restraints: 1.0 (134)
  - Potential type of restraints: upper-bound-parabolic (134)
  - Range of distance target values: 2.7, 4.5 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 212, Sequence coverage: 79.2%
- Total number of restraints: 270
- Total number of restraints per polymer type: 270
- Weight of restraints: 1.0 (270)
- Potential type of restraints: square-well-parabolic (270)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Apoptosis

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Found 1 Document (1.65 seconds)

BMRB: 30150

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Bcl-2-like protein 1, : 1 : 14 : 91 entities Detail

Interaction partners 1. Bcl-2-like protein 1, : 87 interactors Detail

Experiments performed 7 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail