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Found 1 Document (0.802 seconds)

BMRB: 36179

5ZOR

Solution structure of centrin4 from Trypanosoma brucei

Authors

Shan, F.Z., Tu, X.M.

Assembly

Centrin, putative

Entity

1. Centrin, putative (polymer, Thiol state: not present), 149 monomers, 16552.47 Da Detail

MAALTDEQIR EAFNLFDADG SGAIDAEEMA LAMKGLGFGD LPRDEVERTV RSMNTNANGL IEYGEFERMV KSRMAQKDSP EEVLKAFQLF DLDKKGKISF ANLKEVAKLL GENPGDDVLQ EMIAEADEDG DGEVSFEEFK SVMMQMRGK

Formula weight

16552.47 Da

Source organism

Trypanosoma brucei brucei TREU927

Exptl. method

solution NMR

Refine. method

distance geometry

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 80.3 %, Completeness (bb): 85.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.3 % (1365 of 1699)	91.3 % (812 of 889)	61.9 % (404 of 653)	94.9 % (149 of 157)
Backbone	85.7 % (761 of 888)	99.0 % (305 of 308)	71.9 % (312 of 434)	98.6 % (144 of 146)
Sidechain	78.0 % (739 of 947)	87.3 % (507 of 581)	64.2 % (228 of 355)	36.4 % (4 of 11)
Aromatic	2.0 % (2 of 98)	4.1 % (2 of 49)	0.0 % (0 of 49)
Methyl	77.1 % (108 of 140)	98.6 % (69 of 70)	55.7 % (39 of 70)

1. Centrin, putative

MAALTDEQIR EAFNLFDADG SGAIDAEEMA LAMKGLGFGD LPRDEVERTV RSMNTNANGL IEYGEFERMV KSRMAQKDSP EEVLKAFQLF DLDKKGKISF ANLKEVAKLL GENPGDDVLQ EMIAEADEDG DGEVSFEEFK SVMMQMRGK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-13C; U-15N] centrin4, 20 mM sodium phosphate, 200 mM sodium chloride, 2 mM DTT, 2 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	centrin4	[U-13C; U-15N]	protein	0.5 mM
2	sodium chloride	natural abundance	salt	200 mM
3	sodium phosphate	natural abundance	buffer	20 mM
4	DTT	natural abundance		2 mM
5	EDTA	natural abundance		2 mM
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

LACS Plot; CA

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

Referencing offset: -0.13 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.13 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.03 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2018-05-26

Citation

Solution structure of TbCentrin4 from Trypanosoma brucei and its interactions with Ca²⁺ and other centrins
Shan, F., Ye, K., Zhang, J., Liao, S., Zhang, X., Xu, C., Tu, X.
Biochem. J. (2018), 475, 3763-3778, PubMed 30389845 , DOI 10.1042/BCJ20180752 , Abstract

Related entities 1. Centrin, putative, : 1 : 299 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_36179_5zor.nef
Input source #2: Coordindates	5zor.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
MAALTDEQIREAFNLFDADGSGAIDAEEMALAMKGLGFGDLPRDEVERTVRSMNTNANGLIEYGEFERMVKSRMAQKDSPEEVLKAFQLFDLDKKGKISF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAALTDEQIREAFNLFDADGSGAIDAEEMALAMKGLGFGDLPRDEVERTVRSMNTNANGLIEYGEFERMVKSRMAQKDSPEEVLKAFQLFDLDKKGKISF

-------110-------120-------130-------140---------
ANLKEVAKLLGENPGDDVLQEMIAEADEDGDGEVSFEEFKSVMMQMRGK
|||||||||||||||||||||||||||||||||||||||||||||||||
ANLKEVAKLLGENPGDDVLQEMIAEADEDGDGEVSFEEFKSVMMQMRGK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	149	0	0	100.0

Content subtype: combined_36179_5zor.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1331		100.0 (chain: A, length: 149)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	1868 (1)	noe	100.0 (chain: A, length: 149)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	237 (1)	hbond	61.7 (chain: A, length: 149)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	291 (291)	.	100.0 (chain: A, length: 149)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 818
  - ¹³C chemical shifts: 368
  - ¹⁵N chemical shifts: 145
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	889	806	90.7
¹³C chemical shifts	653	368	56.4
¹⁵N chemical shifts	164	145	88.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	308	307	99.7
¹³C chemical shifts	298	149	50.0
¹⁵N chemical shifts	146	145	99.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	581	499	85.9
¹³C chemical shifts	355	219	61.7
¹⁵N chemical shifts	18	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	77	96.3
¹³C chemical shifts	80	36	45.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	0	0.0
¹³C chemical shifts	49	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 100.0%
- Total number of restraints: 1868
- Weight of restraints: 1.0 (1868)
- Potential type of restraints: upper-bound-parabolic (1868)
- Range of distance target values: 2.9, 7.0 (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: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 61.7%
  - Total number of restraints: 237
  - Weight of restraints: 1.0 (237)
  - Potential type of restraints: upper-bound-parabolic (237)
  - Range of distance target values: 1.95, 3.05 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 100.0%
- Total number of restraints: 291
- Total number of restraints per polymer type: 291
- Weight of restraints: 1.0 (291)
- Potential type of restraints: square-well-parabolic (291)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords EF-hand, Trypanosoma brucei, calcium binding, centrin

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Found 1 Document (0.802 seconds)

BMRB: 36179

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Centrin, putative, : 1 : 299 entities Detail

Experiments performed 1 experiments Detail

Instrument

Sample

NMR combined restraints 5 contents Detail