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Found 1 Document (0.632 seconds)

BMRB: 15852

2K61

Solution structure of CaM complexed to DAPk peptide

Authors

Bertini, I., Luchinat, C., Parigi, G., Yuan, J.

Assembly

calmodulin

Entity

1. calmodulin (polymer, Thiol state: not present), 148 monomers, 16707.20 Da Detail

ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGD GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

2. CA (non-polymer), 40.078 × 4 Da

Total weight

16867.512 Da

Max. entity weight

16707.2 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, heteronucl_T1_relaxation, heteronucl_T2_relaxation

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 46.1 %, Completeness (bb): 81.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	46.1 % (768 of 1667)	22.4 % (194 of 865)	66.7 % (430 of 645)	91.7 % (144 of 157)
Backbone	81.2 % (718 of 884)	51.8 % (158 of 305)	96.1 % (416 of 433)	98.6 % (144 of 146)
Sidechain	19.8 % (182 of 920)	6.4 % (36 of 560)	41.8 % (146 of 349)	0.0 % (0 of 11)
Aromatic	0.0 % (0 of 100)	0.0 % (0 of 50)	0.0 % (0 of 50)
Methyl	17.6 % (25 of 142)	11.3 % (8 of 71)	23.9 % (17 of 71)

1. calmodulin

ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGD GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-100% 13C; U-100% 15N]		0.4 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
2	calmodulin	[U-100% 15N]		0.4 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	dioxane	methyl carbon	69.46 ppm	external	direct	1.0
¹H	DSS	methyl protons	0.0 ppm	external	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	external	indirect	0.1013291

Referencing offset: 1.14 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	dioxane	methyl carbon	69.46 ppm	external	direct	1.0
¹H	DSS	methyl protons	0.0 ppm	external	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	external	indirect	0.1013291

Referencing offset: 1.14 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	dioxane	methyl carbon	69.46 ppm	external	direct	1.0
¹H	DSS	methyl protons	0.0 ppm	external	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	external	indirect	0.1013291

Referencing offset: 0.13 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 1 models in PDB: 2K61, Strand ID: A Detail

Heteronucl. T₁

136 T₁ values in 1 lists
Coherence Sz, Field strength (¹H) 700.13 MHz, Pressure 1 atm, Temperature 298 K, pH 7.5 Detail

Heteronucl. T₂

136 T₂ values in 1 lists
Coherence S(+,-), Field strength (¹H) 700.13 MHz, Pressure 1 atm, Temperature 298 K, pH 7.5 Detail

Heteronucl. T₁/T₂

136 T₁/T₂ values in 1 lists
Field strength (¹H) 700.13 MHz, Pressure 1 atm, Temperature 298 K, pH 7.5 Detail

Release date

2009-04-03

Citation

Accurate solution structures of proteins from X-ray data and a minimal set of NMR data: calmodulin-peptide complexes as examples
Bertini, I., Kursula, P., Luchinat, C., Parigi, G., Vahokoski, J., Wilmanns, M., Yuan, J.
J. Am. Chem. Soc. (2009), 131, 5134-5144, PubMed 19317469 , DOI 10.1021/ja8080764 , Abstract

Related entities 1. calmodulin, : 1 : 2 : 115 : 181 entities Detail

Interaction partners 1. calmodulin, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 7 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Dihedral angle restraints, RDC restraints	combined_15852_2k61.nef
Input source #2: Coordindates	2k61.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:60:ASP:OD2	3:1:TB:TB	unknown	unknown	n/a
1:67:GLU:OE2	3:1:TB:TB	unknown	unknown	n/a
1:140:GLU:OE2	2:3:CA:CA	unknown	unknown	n/a
1:133:ASP:OD1	2:3:CA:CA	unknown	unknown	n/a
1:104:GLU:OE1	2:2:CA:CA	unknown	unknown	n/a
1:24:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:97:ASN:OD1	2:2:CA:CA	unknown	unknown	n/a
1:31:GLU:OE2	2:1:CA:CA	unknown	unknown	n/a
1:60:ASP:OD1	3:1:TB:TB	unknown	unknown	n/a
1:67:GLU:OE1	3:1:TB:TB	unknown	unknown	n/a
1:62:THR:O	3:1:TB:TB	unknown	unknown	n/a
1:20:ASP:OD2	2:1:CA:CA	unknown	unknown	n/a
1:104:GLU:OE2	2:2:CA:CA	unknown	unknown	n/a
1:140:GLU:OE1	2:3:CA:CA	unknown	unknown	n/a
1:31:GLU:OE1	2:1:CA:CA	unknown	unknown	n/a
1:26:THR:O	2:1:CA:CA	unknown	unknown	n/a
1:135:GLN:O	2:3:CA:CA	unknown	unknown	n/a
1:93:ASP:OD1	2:2:CA:CA	unknown	unknown	n/a
1:99:TYR:O	2:2:CA:CA	unknown	unknown	n/a
1:56:ASP:OD1	3:1:TB:TB	unknown	unknown	n/a
1:95:ASP:OD1	2:2:CA:CA	unknown	unknown	n/a
1:22:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:129:ASP:OD1	2:3:CA:CA	unknown	unknown	n/a
1:131:ASP:OD2	2:3:CA:CA	unknown	unknown	n/a
1:58:ASP:OD2	3:1:TB:TB	unknown	unknown	n/a
1:64:ASP:OD1	3:1:TB:TB	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	TB	TERBIUM(III) ION	None
C	1	CA	CALCIUM ION	None
C	2	CA	CALCIUM ION	None
C	3	CA	CALCIUM ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGDGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGDGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI

-------110-------120-------130-------140--------
SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
||||||||||||||||||||||||||||||||||||||||||||||||
SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	148	0	0	100.0

Content subtype: combined_15852_2k61.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	26		No information
1	Assigned chemical shifts	Ca4CaM	OK	704		98.6 (chain: A, length: 148)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	229 (229)	.	94.6 (chain: A, length: 148)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	214 (214)	.	66.2 (chain: A, length: 148)

Assigned chemical shifts

Saveframe: Ca4CaM
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 98.6%
- Total number of assignments
  - ¹H chemical shifts: 144
  - ¹³C chemical shifts: 416
  - ¹⁵N chemical shifts: 144
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	865	144	16.6
¹³C chemical shifts	645	416	64.5
¹⁵N chemical shifts	163	144	88.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	305	144	47.2
¹³C chemical shifts	296	284	95.9
¹⁵N chemical shifts	146	144	98.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	560	0	0.0
¹³C chemical shifts	349	132	37.8
¹⁵N chemical shifts	17	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	0	0.0
¹³C chemical shifts	80	11	13.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	0	0.0
¹³C chemical shifts	50	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 94.6%
- Total number of restraints: 229
- Total number of restraints per polymer type: 229
- Weight of restraints: 1.0 (229)
- Potential type of restraints: square-well-parabolic (229)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 66.2%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGDGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI
    ||||||||||||||||||| || |||||| |||| |   |||| ||||||              ||| ||||      |||||||||  |||||||
....TEEQIAEFKEAFSLFDKDG.GT.TTKELG.VMRS.G...TEAE.QDMINE..............LTM.ARKM......EEIREAFRV..KDGNGYI
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120-------130-------140--------
SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
|||||| || || |  ||||| || | || ||||||| || ||  |  
SAAELR.VM.NL.E..TDEEV.EM.R.AD.DGDGQVN.EE.VQ..T  
-------110-------120-------130-------140------

Total number of restraints: 214
Potential type of restraints: undefined (214)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords calmodulin, DAPk peptide

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Found 1 Document (0.632 seconds)

BMRB: 15852

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. calmodulin, : 1 : 2 : 115 : 181 entities Detail

Interaction partners 1. calmodulin, : 1 interactors Detail

Experiments performed 7 experiments Detail

Instrument

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NMR combined restraints 4 contents Detail