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BMRB: 27439

6G7G

Sph15

Authors

Coulthard, R.J., Rajasekar, K.V., Hyde, E.I., Smith, L.J.

Assembly

Sph15

Entity

1. Sph15 (polymer, Thiol state: all disulfide bound), 115 monomers, 13562.57 Da Detail

AMGCKEIEIV IKNTLGPSRI LQYHCRSGNT NVGVQYLNFK GTRIIKFKDD GTERSRWNCL FRQGINMKFF TEVEAYRPDL KHPLCGKRYE LSARMDAIYF KMDERPPQPL NKWRS

Formula weight

13562.57 Da

Source organism

Arabidopsis thaliana

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 75.0 %, Completeness (bb): 95.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.0 % (1067 of 1422)	73.5 % (555 of 755)	74.5 % (406 of 545)	86.9 % (106 of 122)
Backbone	95.1 % (645 of 678)	97.4 % (226 of 232)	92.9 % (313 of 337)	97.2 % (106 of 109)
Sidechain	61.6 % (524 of 851)	62.9 % (329 of 523)	61.9 % (195 of 315)	0.0 % (0 of 13)
Aromatic	27.3 % (36 of 132)	47.0 % (31 of 66)	7.8 % (5 of 64)	0.0 % (0 of 2)
Methyl	69.4 % (68 of 98)	69.4 % (34 of 49)	69.4 % (34 of 49)

1. Sph15

AMGCKEIEIV IKNTLGPSRI LQYHCRSGNT NVGVQYLNFK GTRIIKFKDD GTERSRWNCL FRQGINMKFF TEVEAYRPDL KHPLCGKRYE LSARMDAIYF KMDERPPQPL NKWRS

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
1	Sph15	[U-99% 13C; U-99% 15N]		0.3 mM
2	sodium chloride	natural abundance		50 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
3	Sph15	[U-99% 13C; U-99% 15N]		1 mM
4	sodium chloride	natural abundance		50 mM

LACS Plot; CA

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.08 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.92 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6G7G, Strand ID: A Detail

Release date

2018-04-01

Citation

¹H, ¹³C and ¹⁵N NMR assignments of self-incompatibility protein homologue 15 from Arabidopsis thaliana
Coulthard, R.J., Rajasekar, K.V., Hyde, E.I., Smith, L.J.
Biomol. NMR Assign. (2018), 13, 67-70, PubMed 30284185 , DOI 10.1007/s12104-018-9853-0 , Abstract

Related entities 1. Sph15, : 2 : 33 entities Detail

Experiments performed 12 experiments Detail

1 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
1	Sph15	[U-99% 13C; U-99% 15N]		0.3 mM
2	sodium chloride	natural abundance		50 mM

2 3D HN(COCA)CB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
1	Sph15	[U-99% 13C; U-99% 15N]		0.3 mM
2	sodium chloride	natural abundance		50 mM

3 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
1	Sph15	[U-99% 13C; U-99% 15N]		0.3 mM
2	sodium chloride	natural abundance		50 mM

4 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
1	Sph15	[U-99% 13C; U-99% 15N]		0.3 mM
2	sodium chloride	natural abundance		50 mM

5 3D HCACO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
1	Sph15	[U-99% 13C; U-99% 15N]		0.3 mM
2	sodium chloride	natural abundance		50 mM

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
1	Sph15	[U-99% 13C; U-99% 15N]		0.3 mM
2	sodium chloride	natural abundance		50 mM

7 3D HCCH-COSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
1	Sph15	[U-99% 13C; U-99% 15N]		0.3 mM
2	sodium chloride	natural abundance		50 mM

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
1	Sph15	[U-99% 13C; U-99% 15N]		0.3 mM
2	sodium chloride	natural abundance		50 mM

9 3D H(CCO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
3	Sph15	[U-99% 13C; U-99% 15N]		1 mM
4	sodium chloride	natural abundance		50 mM

10 3D 1H-15N TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
3	Sph15	[U-99% 13C; U-99% 15N]		1 mM
4	sodium chloride	natural abundance		50 mM

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
3	Sph15	[U-99% 13C; U-99% 15N]		1 mM
4	sodium chloride	natural abundance		50 mM

12 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.2

#	Name	Isotope labeling	Type	Concentration
3	Sph15	[U-99% 13C; U-99% 15N]		1 mM
4	sodium chloride	natural abundance		50 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_27439_6g7g.nef
Input source #2: Coordindates	6g7g.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:85:CYS:SG	oxidized, CA 54.331, CB 41.71 ppm	oxidized, CA 54.234, CB 45.809 ppm	2.03
A:25:CYS:SG	A:59:CYS:SG	oxidized, CA 55.133, CB 46.205 ppm	oxidized, CA 55.321, CB 51.047 ppm	2.035

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
AMGCKEIEIVIKNTLGPSRILQYHCRSGNTNVGVQYLNFKGTRIIKFKDDGTERSRWNCLFRQGINMKFFTEVEAYRPDLKHPLCGKRYELSARMDAIYF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AMGCKEIEIVIKNTLGPSRILQYHCRSGNTNVGVQYLNFKGTRIIKFKDDGTERSRWNCLFRQGINMKFFTEVEAYRPDLKHPLCGKRYELSARMDAIYF

-------110-----
KMDERPPQPLNKWRS
|||||||||||||||
KMDERPPQPLNKWRS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	115	0	0	100.0

Content subtype: combined_27439_6g7g.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1028		97.4 (chain: A, length: 115)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3256 (1)	noe	96.5 (chain: A, length: 115)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	52 (1)	hbond	24.3 (chain: A, length: 115)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	126 (126)	.	80.9 (chain: A, length: 115)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 97.4%
- Total number of assignments
  - ¹H chemical shifts: 530
  - ¹³C chemical shifts: 393
  - ¹⁵N chemical shifts: 105
- 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: 115, Sequence coverage: 96.5%
- Total number of restraints: 3253
- Weight of restraints: 1.0 (3253)
- Potential type of restraints: square-well-parabolic (3253)
- Range of distance target values: 1.56, 3.73 (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: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 24.3%
  - Total number of restraints: 52
  - Weight of restraints: 1.0 (52)
  - Potential type of restraints: square-well-parabolic (52)
  - Range of distance target values: 2.21, 3.22 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 80.9%
- Total number of restraints: 126
- Total number of restraints per polymer type: 126
- Weight of restraints: 1.0 (126)
- Potential type of restraints: square-well-parabolic (126)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A