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BMRB: 16608

2KQP

NMR Structure of Proinsulin

Authors

Yang, Y., Hua, Q., Mackin, R.B., Weiss, M.A.

Assembly

Proinsulin

Entity

1. Proinsulin (polymer, Thiol state: all disulfide bound), 86 monomers, 9372.524 Da Detail

FVNQHLCGSD LVEALYLVCG ERGFFYTKPT RREAEDLQVG QVELGGGPGA GSLQPLALEG SLQKRGIVEQ CCTSICSLYQ LENYCN

Formula weight

9372.524 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.2 %, Completeness (bb): 78.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.2 % (823 of 966)	93.0 % (466 of 501)	73.4 % (273 of 372)	90.3 % (84 of 93)
Backbone	78.8 % (402 of 510)	93.9 % (169 of 180)	64.4 % (159 of 247)	89.2 % (74 of 83)
Sidechain	93.0 % (494 of 531)	92.5 % (297 of 321)	93.5 % (187 of 200)	100.0 % (10 of 10)
Aromatic	78.8 % (52 of 66)	84.8 % (28 of 33)	72.7 % (24 of 33)
Methyl	98.9 % (93 of 94)	97.9 % (46 of 47)	100.0 % (47 of 47)

1. Proinsulin

FVNQHLCGSD LVEALYLVCG ERGFFYTKPT RREAEDLQVG QVELGGGPGA GSLQPLALEG SLQKRGIVEQ CCTSICSLYQ LENYCN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	proinsulin	[U-100% 13C; U-100% 15N]		0.3 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.2 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.2 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.1 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2010-03-14

Citation

Solution structure of proinsulin: connecting domain flexibility and prohormone processing
Yang, Y., Hua, Q., Liu, J., Shimizu, E.H., Choquette, M.H., Mackin, R.B., Weiss, M.A.
J. Biol. Chem. (2010), 285, 7847-7851, PubMed 20106974 , DOI 10.1074/jbc.C109.084921 , Abstract

Related entities 1. Proinsulin, : 1 : 18 : 133 entities Detail

Interaction partners 1. Proinsulin, : 8 interactors Detail

More details for 8 interactors identified by 8 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker MSL - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	proinsulin	[U-100% 13C; U-100% 15N]		0.3 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker MSL - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	proinsulin	[U-100% 13C; U-100% 15N]		0.3 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Bruker MSL - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	proinsulin	[U-100% 13C; U-100% 15N]		0.3 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 3D HNCACB

Instrument

Bruker MSL - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	proinsulin	[U-100% 13C; U-100% 15N]		0.3 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 3D C(CO)NH

Instrument

Bruker MSL - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	proinsulin	[U-100% 13C; U-100% 15N]		0.3 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

6 3D H(CCO)NH

Instrument

Bruker MSL - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	proinsulin	[U-100% 13C; U-100% 15N]		0.3 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Bruker MSL - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	proinsulin	[U-100% 13C; U-100% 15N]		0.3 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

8 3D 1H-13C NOESY

Instrument

Bruker MSL - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	proinsulin	[U-100% 13C; U-100% 15N]		0.3 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

9 3D HNCO

Instrument

Bruker MSL - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	proinsulin	[U-100% 13C; U-100% 15N]		0.3 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

10 3D HCCH-TOCSY

Instrument

Bruker MSL - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Type	Concentration
1	proinsulin	[U-100% 13C; U-100% 15N]		0.3 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16608_2kqp.nef
Input source #2: Coordindates	2kqp.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
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:7:CYS:SG	A:72:CYS:SG	unknown, CA 53.94 ppm	oxidized, CB 39.17 ppm	2.023
A:19:CYS:SG	A:85:CYS:SG	oxidized, CA 54.22, CB 36.4 ppm	oxidized, CA 53.44, CB 35.64 ppm	2.02
A:71:CYS:SG	A:76:CYS:SG	oxidized, CB 38.69 ppm	oxidized, CB 37.8 ppm	2.02

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------
FVNQHLCGSDLVEALYLVCGERGFFYTKPTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
FVNQHLCGSDLVEALYLVCGERGFFYTKPTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	86	0	0	100.0

Content subtype: combined_16608_2kqp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	830		100.0 (chain: A, length: 86)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1096 (1)	noe	100.0 (chain: A, length: 86)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	97 (97)	.	69.8 (chain: A, length: 86)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 86, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 476
  - ¹³C chemical shifts: 271
  - ¹⁵N chemical shifts: 83
- 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: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 86, Sequence coverage: 100.0%
- Total number of restraints: 1096
- Weight of restraints: 1.0 (1096)
- Potential type of restraints: square-well-parabolic (1096)
- Range of distance target values: 2.25, 4.35 (Å)
- Histogram of 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: 86, Sequence coverage: 69.8%
- Total number of restraints: 97
- Total number of restraints per polymer type: 97
- Weight of restraints: 1.0 (97)
- Potential type of restraints: square-well-parabolic (97)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Proinsulin, NMR, proinsulin