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BMRB: 18356

2MP4

Solution Structure of ADF like UNC-60A Protein of Caenorhabditis elegans

Authors

Shukla, V., Yadav, R., Kabra, A., Kumar, D., Ono, S., Arora, A.

Assembly

ADF like UNC-60A Protein

Entity

1. ADF like UNC-60A Protein (polymer), 165 monomers, 18366.60 Da Detail

MSSGVMVDPD VQTSFQKLSE GRKEYRYIIF KIDENKVIVE AAVTQDQLGI TGDDYDDSSK AAFDKFVEDV KSRTDNLTDC RYAVFDFKFT CSRVGAGTSK MDKIIFLQIC PDGASIKKKM VYASSAAAIK TSLGTGKILQ FQVSDESEMS HKELLNKLGE KYGDH

Formula weight

18366.6 Da

Source organism

Caenorhabditis elegans

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.0 %, Completeness (bb): 99.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.0 % (1829 of 1906)	95.2 % (942 of 989)	97.3 % (724 of 744)	94.2 % (163 of 173)
Backbone	99.3 % (979 of 986)	99.1 % (336 of 339)	99.4 % (481 of 484)	99.4 % (162 of 163)
Sidechain	93.4 % (1003 of 1074)	93.2 % (606 of 650)	95.7 % (396 of 414)	10.0 % (1 of 10)
Aromatic	86.3 % (126 of 146)	87.7 % (64 of 73)	84.9 % (62 of 73)
Methyl	99.4 % (167 of 168)	98.8 % (83 of 84)	100.0 % (84 of 84)

1. entity

MSSGVMVDPD VQTSFQKLSE GRKEYRYIIF KIDENKVIVE AAVTQDQLGI TGDDYDDSSK AAFDKFVEDV KSRTDNLTDC RYAVFDFKFT CSRVGAGTSK MDKIIFLQIC PDGASIKKKM VYASSAAAIK TSLGTGKILQ FQVSDESEMS HKELLNKLGE KYGDH

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N Labeled UNC-60A

#	Name	Isotope labeling	Concentration
1	UNC-60A	[U-99% 15N]	0.65 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	D2O	[U-99% 2H]	7 %
6	H2O	natural abundance	93 %

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
7	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	[U-99% 2H]	7 %
12	H2O	natural abundance	93 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
13	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
14	sodium phosphate	natural abundance	20 mM
15	sodium chloride	natural abundance	50 mM
16	sodium azide	natural abundance	0.1 %
17	D2O	natural abundance	100 %

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: -0.36 ppm, Outliers: 2 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: -0.36 ppm, Outliers: 2 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: -0.06 ppm, Outliers: 1 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: 0.14 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2MP4, Strand ID: A Detail

Release date

2013-05-19

Citation

NMR Structure and Backbone dynamics of ADF like UNC-60A protein from Caenorhabditis elegans: its divergence from conventional ADF/cofilin
Shukla, V., Yadav, R., Jain, A., Tripathi, S., Kabra, A., Kumar, D., Ono, S., Arora, A.
J. Biol. Chem.

Related entities 1. ADF like UNC-60A Protein, : 1 : 2 : 198 entities Detail

Interaction partners 1. ADF like UNC-60A Protein, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz NMR facility for Macromolecules MSB Division, CSIR-CDRI Lucknow

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N Labeled UNC-60A

#	Name	Isotope labeling	Concentration
1	UNC-60A	[U-99% 15N]	0.65 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	D2O	[U-99% 2H]	7 %
6	H2O	natural abundance	93 %

2 3D HNCACB

Instrument

Varian INOVA - 600 MHz NMR facility for Macromolecules MSB Division, CSIR-CDRI Lucknow

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
7	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	[U-99% 2H]	7 %
12	H2O	natural abundance	93 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz NMR facility for Macromolecules MSB Division, CSIR-CDRI Lucknow

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
7	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	[U-99% 2H]	7 %
12	H2O	natural abundance	93 %

4 3D HNCO

Instrument

Varian INOVA - 600 MHz NMR facility for Macromolecules MSB Division, CSIR-CDRI Lucknow

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
7	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	[U-99% 2H]	7 %
12	H2O	natural abundance	93 %

5 3D HNCA

Instrument

Varian INOVA - 600 MHz NMR facility for Macromolecules MSB Division, CSIR-CDRI Lucknow

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
7	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	[U-99% 2H]	7 %
12	H2O	natural abundance	93 %

6 3D C(CO)NH

Instrument

Bruker Avance3 - 800 MHz CBMR SGPGI Lucknow

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
7	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	[U-99% 2H]	7 %
12	H2O	natural abundance	93 %

7 3D H(CCO)NH

Instrument

Bruker Avance3 - 800 MHz CBMR SGPGI Lucknow

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
7	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	[U-99% 2H]	7 %
12	H2O	natural abundance	93 %

8 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz NMR facility for Macromolecules MSB Division, CSIR-CDRI Lucknow

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
13	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
14	sodium phosphate	natural abundance	20 mM
15	sodium chloride	natural abundance	50 mM
16	sodium azide	natural abundance	0.1 %
17	D2O	natural abundance	100 %

9 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance3 - 800 MHz CBMR SGPGI Lucknow

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
13	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
14	sodium phosphate	natural abundance	20 mM
15	sodium chloride	natural abundance	50 mM
16	sodium azide	natural abundance	0.1 %
17	D2O	natural abundance	100 %

10 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance3 - 800 MHz CBMR SGPGI Lucknow

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
13	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
14	sodium phosphate	natural abundance	20 mM
15	sodium chloride	natural abundance	50 mM
16	sodium azide	natural abundance	0.1 %
17	D2O	natural abundance	100 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance3 - 800 MHz CBMR SGPGI Lucknow

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N Labeled UNC-60A

#	Name	Isotope labeling	Concentration
1	UNC-60A	[U-99% 15N]	0.65 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	D2O	[U-99% 2H]	7 %
6	H2O	natural abundance	93 %

12 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance3 - 800 MHz CBMR SGPGI Lucknow

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
13	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
14	sodium phosphate	natural abundance	20 mM
15	sodium chloride	natural abundance	50 mM
16	sodium azide	natural abundance	0.1 %
17	D2O	natural abundance	100 %

13 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance3 - 800 MHz CBMR SGPGI Lucknow

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
13	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
14	sodium phosphate	natural abundance	20 mM
15	sodium chloride	natural abundance	50 mM
16	sodium azide	natural abundance	0.1 %
17	D2O	natural abundance	100 %

14 2D CB(CGCDCE)HE

Instrument

Varian INOVA - 600 MHz NMR facility for Macromolecules MSB Division, CSIR-CDRI Lucknow

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
7	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	[U-99% 2H]	7 %
12	H2O	natural abundance	93 %

15 2D CB(CGCD)HD

Instrument

Varian INOVA - 600 MHz NMR facility for Macromolecules MSB Division, CSIR-CDRI Lucknow

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
7	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	[U-99% 2H]	7 %
12	H2O	natural abundance	93 %

16 3D HNCACO

Instrument

Varian INOVA - 600 MHz NMR facility for Macromolecules MSB Division, CSIR-CDRI Lucknow

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N, 13C Labeled UNC-60A

#	Name	Isotope labeling	Concentration
7	UNC-60A	[U-99% 13C; U-99% 15N]	0.65 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	sodium azide	natural abundance	0.1 %
11	D2O	[U-99% 2H]	7 %
12	H2O	natural abundance	93 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18356_2mp4.nef
Input source #2: Coordindates	2mp4.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
MSSGVMVDPDVQTSFQKLSEGRKEYRYIIFKIDENKVIVEAAVTQDQLGITGDDYDDSSKAAFDKFVEDVKSRTDNLTDCRYAVFDFKFTCSRVGAGTSK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSSGVMVDPDVQTSFQKLSEGRKEYRYIIFKIDENKVIVEAAVTQDQLGITGDDYDDSSKAAFDKFVEDVKSRTDNLTDCRYAVFDFKFTCSRVGAGTSK

-------110-------120-------130-------140-------150-------160-----
MDKIIFLQICPDGASIKKKMVYASSAAAIKTSLGTGKILQFQVSDESEMSHKELLNKLGEKYGDH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDKIIFLQICPDGASIKKKMVYASSAAAIKTSLGTGKILQFQVSDESEMSHKELLNKLGEKYGDH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	165	0	0	100.0

Content subtype: combined_18356_2mp4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1827		100.0 (chain: A, length: 165)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3432 (1)	noe	99.4 (chain: A, length: 165)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	12 (1)	hbond	6.1 (chain: A, length: 165)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	266 (266)	.	98.2 (chain: A, length: 165)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 946
  - ¹³C chemical shifts: 719
  - ¹⁵N chemical shifts: 162
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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)
151	HIS	HE2	6.34
165	HIS	HE2	7.17

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	989	943	95.3
¹³C chemical shifts	744	719	96.6
¹⁵N chemical shifts	178	162	91.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	339	337	99.4
¹³C chemical shifts	330	326	98.8
¹⁵N chemical shifts	163	162	99.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	650	606	93.2
¹³C chemical shifts	414	393	94.9
¹⁵N chemical shifts	15	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	84	94.4
¹³C chemical shifts	89	84	94.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	62	84.9
¹³C chemical shifts	73	61	83.6

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 99.4%
- Total number of restraints: 3418
- Weight of restraints: 1.0 (3418)
- Potential type of restraints: square-well-parabolic (3418)
- Range of distance target values: 2.0, 3.25 (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_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 6.1%
  - Total number of restraints: 12
  - Weight of restraints: 1.0 (12)
  - Potential type of restraints: square-well-parabolic (12)
  - Range of distance target values: 2.25, 2.25 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 98.2%
- Total number of restraints: 266
- Total number of restraints per polymer type: 266
- Weight of restraints: 1.0 (266)
- Potential type of restraints: square-well-parabolic (266)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ADF/cofilin protein, NMR

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Found 1 Document (0.811 seconds)

BMRB: 18356

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. ADF like UNC-60A Protein, : 1 : 2 : 198 entities Detail

Interaction partners 1. ADF like UNC-60A Protein, : 2 interactors Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 5 contents Detail