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BMRB: 19283

2M96

Solution NMR structure of the RXFP2 LDLa module

Authors

Petrie, E.J., Gooley, P.R., Bathgate, R.A.D.

Assembly

RXFP2 LDLa

Entity

1. RXFP2 LDLa (polymer), 44 monomers, 4641.141 Da Detail

GSMITPSCQK GYFPCGNLTK CLPRAFHCDG KDDCGNGADE ENCG

2. CALCIUM ION (non-polymer), 40.078 Da

Total weight

4681.219 Da

Max. entity weight

4641.141 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 83.0 %, Completeness (bb): 78.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.0 % (382 of 460)	95.9 % (231 of 241)	62.1 % (108 of 174)	95.6 % (43 of 45)
Backbone	78.7 % (203 of 258)	95.7 % (88 of 92)	60.8 % (76 of 125)	95.1 % (39 of 41)
Sidechain	89.1 % (213 of 239)	96.0 % (143 of 149)	76.7 % (66 of 86)	100.0 % (4 of 4)
Aromatic	50.0 % (16 of 32)	87.5 % (14 of 16)	12.5 % (2 of 16)
Methyl	90.0 % (18 of 20)	100.0 % (10 of 10)	80.0 % (8 of 10)

1. RXFP2 LDLa

GSMITPSCQK GYFPCGNLTK CLPRAFHCDG KDDCGNGADE ENCG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	RXFP2_LDLa	[U-99% 15N]		2.0 mM
2	imidazole	natural abundance		50 mM
3	CALCIUM ION	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	RXFP2_LDLa	[U-99% 13C; U-99% 15N]		2.5 mM
7	imidazole	natural abundance		50 mM
8	CALCIUM ION	natural abundance		10 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
11	RXFP2_LDLa	natural abundance		0.5 mM
12	imidazole	[U-2H]		50 mM
13	CALCIUM ION	natural abundance		10 mM
14	H2O	natural abundance		90 %
15	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M96, Strand ID: A Detail

Release date

2014-06-01

Citation

The NMR solution structure of the relaxin (RXFP1) receptor lipoprotein receptor class A module and identification of key residues in the N-terminal region of the module that mediate receptor activation
Petrie, E.J., Gooley, P.R., Bathgate, R.A.D.
J. Biol. Chem. (2007), 282, 4172-4184, PubMed 17148455 , DOI 10.1074/jbc.M609526200 , Abstract

Related entities 1. RXFP2 LDLa, : 1 : 2 : 760 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	RXFP2_LDLa	[U-99% 15N]		2.0 mM
2	imidazole	natural abundance		50 mM
3	CALCIUM ION	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	RXFP2_LDLa	[U-99% 13C; U-99% 15N]		2.5 mM
7	imidazole	natural abundance		50 mM
8	CALCIUM ION	natural abundance		10 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

3 3D C(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	RXFP2_LDLa	[U-99% 13C; U-99% 15N]		2.5 mM
7	imidazole	natural abundance		50 mM
8	CALCIUM ION	natural abundance		10 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

4 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	RXFP2_LDLa	[U-99% 13C; U-99% 15N]		2.5 mM
7	imidazole	natural abundance		50 mM
8	CALCIUM ION	natural abundance		10 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

5 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	RXFP2_LDLa	[U-99% 15N]		2.0 mM
2	imidazole	natural abundance		50 mM
3	CALCIUM ION	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

6 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	RXFP2_LDLa	[U-99% 15N]		2.0 mM
2	imidazole	natural abundance		50 mM
3	CALCIUM ION	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	RXFP2_LDLa	[U-99% 13C; U-99% 15N]		2.5 mM
7	imidazole	natural abundance		50 mM
8	CALCIUM ION	natural abundance		10 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

8 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
6	RXFP2_LDLa	[U-99% 13C; U-99% 15N]		2.5 mM
7	imidazole	natural abundance		50 mM
8	CALCIUM ION	natural abundance		10 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

9 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	RXFP2_LDLa	[U-99% 15N]		2.0 mM
2	imidazole	natural abundance		50 mM
3	CALCIUM ION	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

10 3D HNHB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	RXFP2_LDLa	[U-99% 15N]		2.0 mM
2	imidazole	natural abundance		50 mM
3	CALCIUM ION	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

11 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
11	RXFP2_LDLa	natural abundance		0.5 mM
12	imidazole	[U-2H]		50 mM
13	CALCIUM ION	natural abundance		10 mM
14	H2O	natural abundance		90 %
15	D2O	natural abundance		10 %

12 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
11	RXFP2_LDLa	natural abundance		0.5 mM
12	imidazole	[U-2H]		50 mM
13	CALCIUM ION	natural abundance		10 mM
14	H2O	natural abundance		90 %
15	D2O	natural abundance		10 %

13 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	RXFP2_LDLa	[U-99% 15N]		2.0 mM
2	imidazole	natural abundance		50 mM
3	CALCIUM ION	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19283_2m96.nef
Input source #2: Coordindates	2m96.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:8:CYS:SG	A:21:CYS:SG	oxidized, CA 52.736, CB 40.977 ppm	oxidized, CA 54.861, CB 45.734 ppm	1.988
A:15:CYS:SG	A:34:CYS:SG	oxidized, CA 55.136, CB 38.087 ppm	oxidized, CA 58.015, CB 41.263 ppm	1.996
A:28:CYS:SG	A:43:CYS:SG	oxidized, CA 56.365, CB 36.346 ppm	oxidized, CA 55.003, CB 39.436 ppm	1.994

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)
1:29:ASP:OD2	2:1:CA:CA	unknown	unknown	n/a
1:39:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:33:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:40:GLU:OE1	2:1:CA:CA	unknown	unknown	n/a
1:29:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:39:ASP:OD2	2:1:CA:CA	unknown	unknown	n/a
1:33:ASP:OD2	2:1:CA:CA	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

--------10--------20--------30--------40----
GSMITPSCQKGYFPCGNLTKCLPRAFHCDGKDDCGNGADEENCG
||||||||||||||||||||||||||||||||||||||||||||
GSMITPSCQKGYFPCGNLTKCLPRAFHCDGKDDCGNGADEENCG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	44	0	0	100.0

Content subtype: combined_19283_2m96.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	10		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	384		100.0 (chain: A, length: 44)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	456 (1)	noe	95.5 (chain: A, length: 44)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	4 (1)	undefined	No information
3	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	6 (1)	noe	No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 234
  - ¹³C chemical shifts: 107
  - ¹⁵N chemical shifts: 43
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 95.5%
- Total number of restraints: 456
- Weight of restraints: 1.0 (456)
- Potential type of restraints: upper-bound-parabolic (456)
- Range of distance target values: 2.57, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: OK
  - Experiment type: undefined
  - Total number of restraints: 4
  - Weight of restraints: 1.0 (4)
  - Potential type of restraints: upper-bound-parabolic (4)
  - Range of distance target values: 3.04, 3.8 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_4
    - Status: OK
    - Experiment type: noe
    - Total number of restraints: 6
    - Weight of restraints: 1.0 (6)
    - Potential type of restraints: upper-bound-parabolic (6)
    - Range of distance target values: 3.2, 3.88 (Å)
    - Histogram of distance target values
    - Histogram of discrepancy in distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map

Keywords INSL3 receptor, LDL Class A module, RXFP2, signaling