BMRBj - BMREntryMaster

Found 1 Document (0.674 seconds)

BMRB: 19633

2MHH

Solution structure of a EF-hand domain from sea urchin polycystin-2

Authors

Kuo, I.Y., Keeler, C., Corbin, R., Celic, A., Petri, E.T., Hodsdon, M.E., Ehrlich, B.E.

Assembly

EF-hand domain from sea urchin polycystin-2

Entity

1. EF-hand domain from sea urchin polycystin-2 (polymer, Thiol state: all free), 96 monomers, 10728.62 Da Detail

GGLVPRGSHM ASKRDKIADI QEALAHADAN ADQHLDFDEW RQELKCRGHA DADIEAVFAK YDVDGDRVLD AEEQMKMAHD LEGQKSDLNN QLAELE

Formula weight

10728.62 Da

Source organism

Strongylocentrotus purpuratus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.0 %, Completeness: 93.6 %, Completeness (bb): 97.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.6 % (998 of 1066)	91.2 % (506 of 555)	95.6 % (388 of 406)	99.0 % (104 of 105)
Backbone	97.9 % (562 of 574)	95.9 % (189 of 197)	98.9 % (279 of 282)	98.9 % (94 of 95)
Sidechain	90.4 % (526 of 582)	88.5 % (317 of 358)	93.0 % (199 of 214)	100.0 % (10 of 10)
Aromatic	70.0 % (42 of 60)	76.7 % (23 of 30)	62.1 % (18 of 29)	100.0 % (1 of 1)
Methyl	100.0 % (92 of 92)	100.0 % (46 of 46)	100.0 % (46 of 46)

1. entity

GGLVPRGSHM ASKRDKIADI QEALAHADAN ADQHLDFDEW RQELKCRGHA DADIEAVFAK YDVDGDRVLD AEEQMKMAHD LEGQKSDLNN QLAELE

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

LACS Plot; CA

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.02 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 0.21 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2014-04-10

Citation

The number and location of EF hand motifs dictates the calcium dependence of polycystin-2 function
Kuo, I.Y., Keeler, C., Corbin, R., Celic, A., Petri, E.T., Hodsdon, M.E., Ehrlich, B.E.
FASEB J. (2014), 28, 2332-2346, PubMed 24558196 , DOI 10.1096/fj.13-247106 , Abstract

Related entities 1. EF-hand domain from sea urchin polycystin-2, : 1 : 26 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

3 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

5 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

6 3D HN(CA)CO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

7 3D HCACO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

8 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

9 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

10 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

11 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

12 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

13 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

14 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.38

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.7 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		150 mM
4	calcium chloride	natural abundance		20 mM
5	TCEP	natural abundance		5 mM
6	sodium azide	natural abundance		.05 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_19633_2mhh.nef
Input source #2: Coordindates	2mhh.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

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	96	0	0	100.0

Content subtype: combined_19633_2mhh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	994		99.0 (chain: A, length: 96)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2601 (1)	noe	99.0 (chain: A, length: 96)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	156 (156)	.	87.5 (chain: A, length: 96)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	124 (124)	.	80.2 (chain: A, length: 96)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 99.0%
- Total number of assignments
  - ¹H chemical shifts: 504
  - ¹³C chemical shifts: 386
  - ¹⁵N chemical shifts: 104
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 99.0%
- Total number of restraints: 2496
- Weight of restraints: 1.0 (2496)
- Potential type of restraints: square-well-parabolic (2496)
- Range of distance target values: 3.31, 4.65 (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: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 87.5%
- Total number of restraints: 156
- Total number of restraints per polymer type: 156
- Weight of restraints: 1.0 (156)
- Potential type of restraints: square-well-parabolic (156)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 80.2%

-------20--------30--------40--------50--------60--------70--------80--------90-------100-------
GGLVPRGSHMASKRDKIADIQEALAHADANADQHLDFDEWRQELKCRGHADADIEAVFAKYDVDGDRVLDAEEQMKMAHDLEGQKSDLNNQLAELE
          |||    ||||||||||||||||||||||||||||||||| |||||||||||||||| |||| ||||| ||||||| |||||||||
..........ASK....ADIQEALAHADANADQHLDFDEWRQELKCRGHA.ADIEAVFAKYDVDGDR.LDAE.QMKMA.DLEGQKS.LNNQLAELE

Total number of restraints: 124
Potential type of restraints: undefined (124)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords Calcium, Channel, EF-hand