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Found 1 Document (0.777 seconds)

BMRB: 25905

2N9G

Solution structure of the bromodomain of Trypanosoma brucei Bromodomain Factor 2(BDF2)

Authors

Yang, X.

Assembly

bromodomain of Trypanosoma brucei Bromodomain Factor 2(BDF2)

Entity

1. bromodomain of Trypanosoma brucei Bromodomain Factor 2(BDF2) (polymer, Thiol state: all free), 111 monomers, 12706.13 Da Detail

MSKNERDTSF NKNGCLVFVS RLWDLDKLGM FHHPVSAEEL PDYHTVIKRP VDLSSIRDGI EKGTYATDVD VQNDVARMIT NALEYNAKGS TWYQEAMSFR KTYLDLARQS G

Formula weight

12706.13 Da

Source organism

Trypanosoma brucei

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 67.1 %, Completeness (bb): 80.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	67.1 % (867 of 1292)	66.0 % (442 of 670)	62.2 % (313 of 503)	94.1 % (112 of 119)
Backbone	80.8 % (533 of 660)	93.3 % (210 of 225)	67.3 % (220 of 327)	95.4 % (103 of 108)
Sidechain	59.0 % (435 of 737)	52.1 % (232 of 445)	69.0 % (194 of 281)	81.8 % (9 of 11)
Aromatic	10.3 % (12 of 116)	10.3 % (6 of 58)	7.1 % (4 of 56)	100.0 % (2 of 2)
Methyl	82.1 % (92 of 112)	82.1 % (46 of 56)	82.1 % (46 of 56)

1. entity

MSKNERDTSF NKNGCLVFVS RLWDLDKLGM FHHPVSAEEL PDYHTVIKRP VDLSSIRDGI EKGTYATDVD VQNDVARMIT NALEYNAKGS TWYQEAMSFR KTYLDLARQS G

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	0.5 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	20 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

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: -0.28 ppm, Outliers: 1 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: -0.28 ppm, Outliers: 1 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: 0.1 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N9G, Strand ID: A Detail

Release date

2016-11-16

Citation

Solution structure of the bromodomain of Trypanosoma brucei Bromodomain Factor 2(BDF2)
Yang, X.
Not known

Related entities 1. bromodomain of Trypanosoma brucei Bromodomain Factor 2(BDF2), : 1 : 1 : 1 : 114 entities Detail

Experiments performed 1 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25905_2n9g.nef
Input source #2: Coordindates	2n9g.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
MSKNERDTSFNKNGCLVFVSRLWDLDKLGMFHHPVSAEELPDYHTVIKRPVDLSSIRDGIEKGTYATDVDVQNDVARMITNALEYNAKGSTWYQEAMSFR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSKNERDTSFNKNGCLVFVSRLWDLDKLGMFHHPVSAEELPDYHTVIKRPVDLSSIRDGIEKGTYATDVDVQNDVARMITNALEYNAKGSTWYQEAMSFR

-------110-
KTYLDLARQSG
|||||||||||
KTYLDLARQSG

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_25905_2n9g.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	821		99.1 (chain: A, length: 111)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	993 (1)	noe	99.1 (chain: A, length: 111)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	68 (1)	hbond	45.0 (chain: A, length: 111)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	161 (161)	.	91.0 (chain: A, length: 111)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 417
  - ¹³C chemical shifts: 292
  - ¹⁵N chemical shifts: 112
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	670	417	62.2
¹³C chemical shifts	503	292	58.1
¹⁵N chemical shifts	126	112	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	225	206	91.6
¹³C chemical shifts	222	108	48.6
¹⁵N chemical shifts	108	103	95.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	445	211	47.4
¹³C chemical shifts	281	184	65.5
¹⁵N chemical shifts	18	9	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	42	70.0
¹³C chemical shifts	60	41	68.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	2	3.4
¹³C chemical shifts	56	0	0.0
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- 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: 993
- Weight of restraints: 1.0 (993)
- Potential type of restraints: square-well-parabolic (993)
- Range of distance target values: 2.6, 4.3 (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_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 45.0%
  - Total number of restraints: 68
  - Weight of restraints: 1.0 (68)
  - Potential type of restraints: square-well-parabolic (68)
  - Range of distance target values: 2.0, 3.5 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 91.0%
- Total number of restraints: 161
- Total number of restraints per polymer type: 161
- Weight of restraints: 1.0 (161)
- Potential type of restraints: square-well-parabolic (161)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (0.777 seconds)

BMRB: 25905

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. bromodomain of Trypanosoma brucei Bromodomain Factor 2(BDF2), : 1 : 1 : 1 : 114 entities Detail

Experiments performed 1 experiments Detail

Instrument

Sample

NMR combined restraints 5 contents Detail