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BMRB: 30209

5U87

NMR structure of the precursor protein PawS1 comprising SFTI-1 and a seed storage albumin

Authors

Franke, B., James, A.M., Mobli, M., Colgrave, M.L., Mylne, J.S., Rosengren, K.J.

Assembly

Preproalbumin PawS1

Entity

1. Preproalbumin PawS1 (polymer), 116 monomers, 13265.21 Da Detail

GRCTKSIPPI CFPDGLDNPR GCQIRIQQLN HCQMHLTSFD YKLRMAVENP KQQQHLSLCC NQLQEVEKQC QCEAIKQVVE QAQKQLQQGQ GGQQQVQQMV KKAQMLPNQC NLQCSI

Formula weight

13265.21 Da

Source organism

Helianthus annuus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.6 %, Completeness (bb): 98.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.6 % (1284 of 1401)	90.7 % (682 of 752)	96.1 % (487 of 507)	81.0 % (115 of 142)
Backbone	98.4 % (673 of 684)	98.7 % (229 of 232)	97.7 % (334 of 342)	100.0 % (110 of 110)
Sidechain	87.2 % (721 of 827)	87.1 % (453 of 520)	95.6 % (263 of 275)	15.6 % (5 of 32)
Aromatic	85.0 % (34 of 40)	95.0 % (19 of 20)	75.0 % (15 of 20)
Methyl	95.0 % (95 of 100)	96.0 % (48 of 50)	94.0 % (47 of 50)

1. entity 1

GRCTKSIPPI CFPDGLDNPR GCQIRIQQLN HCQMHLTSFD YKLRMAVENP KQQQHLSLCC NQLQEVEKQC QCEAIKQVVE QAQKQLQQGQ GGQQQVQQMV KKAQMLPNQC NLQCSI

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 4.62, Details 3.9 mg/mL [U-13C; U-15N] Proalbumin PawS1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Proalbumin PawS1	[U-13C; U-15N]		3.9 mg/mL

LACS Plot; CA

Referencing offset: 0.06 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: 0.06 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: 0.1 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.13 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5U87, Strand ID: A Detail

Release date

2017-02-01

Related entities 1. Preproalbumin PawS1, : 1 : 9 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 4.62, Details 3.9 mg/mL [U-13C; U-15N] Proalbumin PawS1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Proalbumin PawS1	[U-13C; U-15N]		3.9 mg/mL

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 4.62, Details 3.9 mg/mL [U-13C; U-15N] Proalbumin PawS1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Proalbumin PawS1	[U-13C; U-15N]		3.9 mg/mL

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 4.62, Details 3.9 mg/mL [U-13C; U-15N] Proalbumin PawS1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Proalbumin PawS1	[U-13C; U-15N]		3.9 mg/mL

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 4.62, Details 3.9 mg/mL [U-13C; U-15N] Proalbumin PawS1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Proalbumin PawS1	[U-13C; U-15N]		3.9 mg/mL

5 3D HNCO

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 4.62, Details 3.9 mg/mL [U-13C; U-15N] Proalbumin PawS1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Proalbumin PawS1	[U-13C; U-15N]		3.9 mg/mL

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 4.62, Details 3.9 mg/mL [U-13C; U-15N] Proalbumin PawS1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Proalbumin PawS1	[U-13C; U-15N]		3.9 mg/mL

7 3D H(CC)(CO)NH-TOCSY

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 4.62, Details 3.9 mg/mL [U-13C; U-15N] Proalbumin PawS1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Proalbumin PawS1	[U-13C; U-15N]		3.9 mg/mL

8 3D (H)CC(CO)NH-TOCSY

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 4.62, Details 3.9 mg/mL [U-13C; U-15N] Proalbumin PawS1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Proalbumin PawS1	[U-13C; U-15N]		3.9 mg/mL

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 4.62, Details 3.9 mg/mL [U-13C; U-15N] Proalbumin PawS1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Proalbumin PawS1	[U-13C; U-15N]		3.9 mg/mL

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 4.62, Details 3.9 mg/mL [U-13C; U-15N] Proalbumin PawS1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Proalbumin PawS1	[U-13C; U-15N]		3.9 mg/mL

11 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 4.62, Details 3.9 mg/mL [U-13C; U-15N] Proalbumin PawS1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Proalbumin PawS1	[U-13C; U-15N]		3.9 mg/mL

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30209_5u87.nef
Input source #2: Coordindates	5u87.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:3:CYS:SG	A:11:CYS:SG	oxidized, CA 55.445, CB 48.472 ppm	oxidized, CA 55.033, CB 46.367 ppm	2.033
A:22:CYS:SG	A:70:CYS:SG	oxidized, CA 55.683, CB 40.877 ppm	oxidized, CA 54.851, CB 42.402 ppm	2.034
A:32:CYS:SG	A:59:CYS:SG	oxidized, CA 56.861, CB 39.048 ppm	oxidized, CA 58.175, CB 37.175 ppm	2.038
A:60:CYS:SG	A:110:CYS:SG	oxidized 36.4%, reduced 63.6%, CA 55.388, CB 32.148 ppm	oxidized 98.2%, reduced 1.8%, CA 50.916, CB 34.432 ppm	2.035
A:72:CYS:SG	A:114:CYS:SG	oxidized, CA 62.901, CB 37.439 ppm	oxidized, CA 53.495, CB 43.133 ppm	2.034

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
GRCTKSIPPICFPDGLDNPRGCQIRIQQLNHCQMHLTSFDYKLRMAVENPKQQQHLSLCCNQLQEVEKQCQCEAIKQVVEQAQKQLQQGQGGQQQVQQMV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GRCTKSIPPICFPDGLDNPRGCQIRIQQLNHCQMHLTSFDYKLRMAVENPKQQQHLSLCCNQLQEVEKQCQCEAIKQVVEQAQKQLQQGQGGQQQVQQMV

-------110------
KKAQMLPNQCNLQCSI
||||||||||||||||
KKAQMLPNQCNLQCSI

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	116	0	0	100.0

Content subtype: combined_30209_5u87.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1262		100.0 (chain: A, length: 116)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	3772 (1)	noe	100.0 (chain: A, length: 116)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	68 (1)	hbond	44.8 (chain: A, length: 116)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	Warning	207 (207)	.	96.6 (chain: A, length: 116)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 671
  - ¹³C chemical shifts: 482
  - ¹⁵N chemical shifts: 109
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 100.0%
- Total number of restraints: 3772
- Weight of restraints: 1.0 (3772)
- Potential type of restraints: upper-bound-parabolic (3772)
- Range of distance target values: 2.19, 5.5 (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: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 44.8%
  - Total number of restraints: 68
  - Weight of restraints: 1.0 (68)
  - Potential type of restraints: square-well-parabolic (68)
  - Range of distance target values: 1.15, 1.65 (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_2
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 96.6%
- Total number of restraints: 207
- Total number of restraints per polymer type: 207
- Weight of restraints: 1.0 (207)
- Potential type of restraints: square-well-parabolic (207)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PLANT PROTEIN, SFTI-1, Structure from MOLMOL, seed storage albumin, trypsin inhibitor