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BMRB: 18710

2LY6

Refined solution structure of recombinant brazzein at low temperature

Authors

Cornilescu, C.C., Cornilescu, G., Tonelli, M., Markley, J.L., Assadi-Porter, F.M.

Assembly

recombinant brazzein

Entity

1. recombinant brazzein (polymer), 53 monomers, 6370.146 Da Detail

DKCKKVYENY PVSKCQLANQ CNYDCKLDKH ARSGECFYDE KRNLQCICDY CEY

Formula weight

6370.146 Da

Source organism

Pentadiplandra brazzeana

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.3 %, Completeness (bb): 97.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.3 % (586 of 635)	90.8 % (306 of 337)	93.3 % (223 of 239)	96.6 % (57 of 59)
Backbone	97.8 % (309 of 316)	98.1 % (104 of 106)	98.1 % (155 of 158)	96.2 % (50 of 52)
Sidechain	88.7 % (329 of 371)	87.4 % (202 of 231)	90.2 % (120 of 133)	100.0 % (7 of 7)
Aromatic	58.1 % (36 of 62)	58.1 % (18 of 31)	58.1 % (18 of 31)
Methyl	100.0 % (28 of 28)	100.0 % (14 of 14)	100.0 % (14 of 14)

1. entity

DKCKKVYENY PVSKCQLANQ CNYDCKLDKH ARSGECFYDE KRNLQCICDY CEY

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	brazzein	[U-13C; U-15N]		1.0 ~ 2.0 (±0.1) mM
2	sodium chloride	natural abundance		5 (±0.1) mM
3	H2O	natural abundance		93 %
4	D2O	natural abundance		7 %

LACS Plot; CA

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.11 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.19 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 2LY6, Strand ID: A Detail

Release date

2012-10-14

Citation

Temperature-dependent conformational change affecting Tyr11 and sweetness loops of brazzein
Cornilescu, C.C., Cornilescu, G., Rao, H., Porter, S.F., Tonelli, M., Derider, M.L., Markley, J.L., Assadi-Porter, F.M.
Proteins (2013), 81, 919-925, PubMed 23349025 , DOI 10.1002/prot.24259 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 16215 released on 2013-01-27
Title Refined solution structure of des-pyro Glu brazzein

Related entities 1. recombinant brazzein, : 1 : 7 : 2 : 5 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	brazzein	[U-13C; U-15N]		1.0 ~ 2.0 (±0.1) mM
2	sodium chloride	natural abundance		5 (±0.1) mM
3	H2O	natural abundance		93 %
4	D2O	natural abundance		7 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	brazzein	[U-13C; U-15N]		1.0 ~ 2.0 (±0.1) mM
2	sodium chloride	natural abundance		5 (±0.1) mM
3	H2O	natural abundance		93 %
4	D2O	natural abundance		7 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	brazzein	[U-13C; U-15N]		1.0 ~ 2.0 (±0.1) mM
2	sodium chloride	natural abundance		5 (±0.1) mM
3	H2O	natural abundance		93 %
4	D2O	natural abundance		7 %

4 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	brazzein	[U-13C; U-15N]		1.0 ~ 2.0 (±0.1) mM
2	sodium chloride	natural abundance		5 (±0.1) mM
3	H2O	natural abundance		93 %
4	D2O	natural abundance		7 %

5 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	brazzein	[U-13C; U-15N]		1.0 ~ 2.0 (±0.1) mM
2	sodium chloride	natural abundance		5 (±0.1) mM
3	H2O	natural abundance		93 %
4	D2O	natural abundance		7 %

6 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	brazzein	[U-13C; U-15N]		1.0 ~ 2.0 (±0.1) mM
2	sodium chloride	natural abundance		5 (±0.1) mM
3	H2O	natural abundance		93 %
4	D2O	natural abundance		7 %

7 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	brazzein	[U-13C; U-15N]		1.0 ~ 2.0 (±0.1) mM
2	sodium chloride	natural abundance		5 (±0.1) mM
3	H2O	natural abundance		93 %
4	D2O	natural abundance		7 %

8 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	brazzein	[U-13C; U-15N]		1.0 ~ 2.0 (±0.1) mM
2	sodium chloride	natural abundance		5 (±0.1) mM
3	H2O	natural abundance		93 %
4	D2O	natural abundance		7 %

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	brazzein	[U-13C; U-15N]		1.0 ~ 2.0 (±0.1) mM
2	sodium chloride	natural abundance		5 (±0.1) mM
3	H2O	natural abundance		93 %
4	D2O	natural abundance		7 %

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	brazzein	[U-13C; U-15N]		1.0 ~ 2.0 (±0.1) mM
2	sodium chloride	natural abundance		5 (±0.1) mM
3	H2O	natural abundance		93 %
4	D2O	natural abundance		7 %

11 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	brazzein	[U-13C; U-15N]		1.0 ~ 2.0 (±0.1) mM
2	sodium chloride	natural abundance		5 (±0.1) mM
3	H2O	natural abundance		93 %
4	D2O	natural abundance		7 %

12 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.2 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	brazzein	[U-13C; U-15N]		1.0 ~ 2.0 (±0.1) mM
2	sodium chloride	natural abundance		5 (±0.1) mM
3	H2O	natural abundance		93 %
4	D2O	natural abundance		7 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Dihedral angle restraints	combined_18710_2ly6.nef
Input source #2: Coordindates	2ly6.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:4:CYS:SG	A:52:CYS:SG	oxidized, CA 57.281, CB 41.329 ppm	oxidized, CA 55.025, CB 44.241 ppm	2.02
A:16:CYS:SG	A:37:CYS:SG	oxidized, CA 58.052, CB 40.413 ppm	oxidized, CA 56.316, CB 45.938 ppm	2.019
A:22:CYS:SG	A:47:CYS:SG	oxidized, CA 58.392, CB 38.574 ppm	oxidized, CA 55.011, CB 38.063 ppm	2.02
A:22:CYS:SG	A:37:CYS:SG	oxidized, CA 58.392, CB 38.574 ppm	oxidized, CA 56.316, CB 45.938 ppm	2.952
A:26:CYS:SG	A:49:CYS:SG	oxidized, CA 60.528, CB 36.64 ppm	oxidized, CA 51.59, CB 35.534 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----
DKCKKVYENYPVSKCQLANQCNYDCKLDKHARSGECFYDEKRNLQCICDYCEY
|||||||||||||||||||||||||||||||||||||||||||||||||||||
DKCKKVYENYPVSKCQLANQCNYDCKLDKHARSGECFYDEKRNLQCICDYCEY
--------10--------20--------30--------40--------50---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	53	0	0	100.0

Content subtype: combined_18710_2ly6.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	582		100.0 (chain: A, length: 53)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	99 (99)	.	100.0 (chain: A, length: 53)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 300
  - ¹³C chemical shifts: 223
  - ¹⁵N chemical shifts: 59
- 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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 100.0%
- Total number of restraints: 99
- Total number of restraints per polymer type: 99
- Weight of restraints: 1.0 (99)
- Potential type of restraints: square-well-parabolic (99)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords brazzein, CYS-SAIL, NMR, solution