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BMRB: 17621

2Y4Q

Solution structure of the EF-hand domain of Human Polycystin 2

Authors

Allen, M.D., Qamar, S., Sandford, R.N.

Assembly

Solution structure of the EF-hand domain of Human Polycystin 2

Entity

1. POLYCYSTIN-2 (polymer, Thiol state: not present), 79 monomers, 9045.590 Da Detail

GGSLKKNTVD DISESLRQGG GKLNFDELRQ DLKGKGHTDA EIEAIFTKYD QDGDQELTEH EHQQMRDDLE KEREDLDLD

2. CA (non-polymer), 40.078 Da

Total weight

9085.668 Da

Max. entity weight

9045.59 Da

Source organism

Exptl. method

Refine. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 66.0 %, Completeness (bb): 77.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	66.0 % (595 of 901)	76.3 % (363 of 476)	48.2 % (163 of 338)	79.3 % (69 of 87)
Backbone	77.4 % (367 of 474)	92.8 % (154 of 166)	62.9 % (144 of 229)	87.3 % (69 of 79)
Sidechain	58.2 % (290 of 498)	67.4 % (209 of 310)	45.0 % (81 of 180)	0.0 % (0 of 8)
Aromatic	20.0 % (8 of 40)	40.0 % (8 of 20)	0.0 % (0 of 20)
Methyl	35.9 % (23 of 64)	12.5 % (4 of 32)	59.4 % (19 of 32)

1. POLYCYSTIN-2

GGSLKKNTVD DISESLRQGG GKLNFDELRQ DLKGKGHTDA EIEAIFTKYD QDGDQELTEH EHQQMRDDLE KEREDLDLD

Show sample condition

Sample

Solvent system 95% water / 5% D2O, Pressure 1 atm, Temperature 298.000 K, pH 6.500, Details 1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	POLYCYSTIN-2	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Potassium phosphate	natural abundance		20 mM
5	NaCl	natural abundance		100 mM

LACS Plot; CA

Referencing offset: 0.19 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.19 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.01 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2Y4Q, Strand ID: A Detail

Release date

2011-12-19

Related entities 1. POLYCYSTIN-2, : 1 : 8 : 20 entities Detail

Interaction partners 1. POLYCYSTIN-2, : 21 interactors Detail

More details for 21 interactors identified by 9 citations

Experiments performed 11 experiments Detail

1 2D NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water / 5% D2O, Pressure 1 atm, Temperature 298.000 K, pH 6.500, Details 1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	POLYCYSTIN-2	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Potassium phosphate	natural abundance		20 mM
5	NaCl	natural abundance		100 mM

2 2D TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water / 5% D2O, Pressure 1 atm, Temperature 298.000 K, pH 6.500, Details 1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	POLYCYSTIN-2	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Potassium phosphate	natural abundance		20 mM
5	NaCl	natural abundance		100 mM

3 2D DQF COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water / 5% D2O, Pressure 1 atm, Temperature 298.000 K, pH 6.500, Details 1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	POLYCYSTIN-2	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Potassium phosphate	natural abundance		20 mM
5	NaCl	natural abundance		100 mM

4 2D HSQC 15N

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water / 5% D2O, Pressure 1 atm, Temperature 298.000 K, pH 6.500, Details 1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	POLYCYSTIN-2	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Potassium phosphate	natural abundance		20 mM
5	NaCl	natural abundance		100 mM

5 2D HSQC 13C

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water / 5% D2O, Pressure 1 atm, Temperature 298.000 K, pH 6.500, Details 1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	POLYCYSTIN-2	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Potassium phosphate	natural abundance		20 mM
5	NaCl	natural abundance		100 mM

6 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water / 5% D2O, Pressure 1 atm, Temperature 298.000 K, pH 6.500, Details 1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	POLYCYSTIN-2	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Potassium phosphate	natural abundance		20 mM
5	NaCl	natural abundance		100 mM

7 3D CBCACONH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water / 5% D2O, Pressure 1 atm, Temperature 298.000 K, pH 6.500, Details 1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	POLYCYSTIN-2	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Potassium phosphate	natural abundance		20 mM
5	NaCl	natural abundance		100 mM

8 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water / 5% D2O, Pressure 1 atm, Temperature 298.000 K, pH 6.500, Details 1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	POLYCYSTIN-2	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Potassium phosphate	natural abundance		20 mM
5	NaCl	natural abundance		100 mM

9 3D HNCACO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water / 5% D2O, Pressure 1 atm, Temperature 298.000 K, pH 6.500, Details 1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	POLYCYSTIN-2	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Potassium phosphate	natural abundance		20 mM
5	NaCl	natural abundance		100 mM

10 3D HBHACONH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water / 5% D2O, Pressure 1 atm, Temperature 298.000 K, pH 6.500, Details 1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	POLYCYSTIN-2	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Potassium phosphate	natural abundance		20 mM
5	NaCl	natural abundance		100 mM

11 3D HNHB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% water / 5% D2O, Pressure 1 atm, Temperature 298.000 K, pH 6.500, Details 1.5 mM

#	Name	Isotope labeling	Type	Concentration
1	POLYCYSTIN-2	[U-13C; U-15N]		1.5 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	Potassium phosphate	natural abundance		20 mM
5	NaCl	natural abundance		100 mM

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17621_2y4q.nef
Input source #2: Coordindates	2y4q.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)
2:1:CA:CA	1:52:ASP:OD1	unknown	unknown	n/a
2:1:CA:CA	1:54:ASP:OD1	unknown	unknown	n/a
2:1:CA:CA	1:54:ASP:OD2	unknown	unknown	n/a
2:1:CA:CA	1:50:ASP:OD2	unknown	unknown	n/a
2:1:CA:CA	1:56:GLU:O	unknown	unknown	n/a
2:1:CA:CA	1:52:ASP:OD2	unknown	unknown	n/a
2:1:CA:CA	1:61:GLU:OE1	unknown	unknown	n/a
2:1:CA:CA	1:61:GLU:OE2	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CA	CALCIUM ION	None

Sequence alignments

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

----720-------730-------740-------750-------760-------770-------780-------790--
GGSLKKNTVDDISESLRQGGGKLNFDELRQDLKGKGHTDAEIEAIFTKYDQDGDQELTEHEHQQMRDDLEKEREDLDLD
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GGSLKKNTVDDISESLRQGGGKLNFDELRQDLKGKGHTDAEIEAIFTKYDQDGDQELTEHEHQQMRDDLEKEREDLDLD
--------10--------20--------30--------40--------50--------60--------70---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	79	0	0	100.0

Content subtype: combined_17621_2y4q.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	581		100.0 (chain: A, length: 79)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2251 (1)	noe	98.7 (chain: A, length: 79)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	38 (1)	hbond	39.2 (chain: A, length: 79)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	Warning	18 (18)	.	22.8 (chain: A, length: 79)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	134 (134)	.	88.6 (chain: A, length: 79)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_7	OK	50 (50)	.	63.3 (chain: A, length: 79)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 100.0%
- Total number of assignments
  - ¹⁵N chemical shifts: 69
  - ¹H chemical shifts: 360
  - ¹³C chemical shifts: 152
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 98.7%
- Total number of restraints: 2234
- Weight of restraints: 1.0 (2234)
- Potential type of restraints: square-well-parabolic (2234)
- Range of distance target values: 2.3, 3.9 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- 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: 79, Sequence coverage: 39.2%
  - Total number of restraints: 38
  - Weight of restraints: 1.0 (38)
  - Potential type of restraints: square-well-parabolic (38)
  - Range of distance target values: 1.95, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 22.8%
- Total number of restraints: 18
- Total number of restraints per polymer type: 18
- Weight of restraints: 1.0 (18)
- Potential type of restraints: square-well-parabolic (18)
- Dihedral angle restraints per residue
- Saveframe: CNS/XPLOR_dihedral_6
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 88.6%
  - Total number of restraints: 134
  - Total number of restraints per polymer type: 134
  - Weight of restraints: 1.0 (134)
  - Potential type of restraints: square-well-parabolic (134)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_7
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 63.3%
- Total number of restraints: 50
- Potential type of restraints: undefined (50)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords EF-Hand, polycystin 2, TRANSPORT PROTEIN