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BMRB: 19233

2MGP

1H, 13C, 15N assignments for P. yoelii Merozoite Surface Protein 1

Authors

Curd, R.D., Birdsall, B., Kadekoppala, M., Ogun, S.A., Kelly, G., Holder, A.A.

Assembly

msp1

Entity

1. msp1 (polymer, Thiol state: all disulfide bound), 99 monomers, 10718.63 Da Detail

GVDPKHVCVD TRDIPKNAGC FRDDDGTEEW RCLLGYKKGE GNTCVENNNP TCDINNGGCD PTASCQNAES TENSKKIICT CKEPTPNAYY EGVFCSSSS

Formula weight

10718.63 Da

Source organism

Plasmodium yoelii

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.4 %, Completeness (bb): 98.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.4 % (1029 of 1057)	98.4 % (542 of 551)	95.3 % (382 of 401)	100.0 % (105 of 105)
Backbone	98.1 % (571 of 582)	99.0 % (199 of 201)	96.9 % (279 of 288)	100.0 % (93 of 93)
Sidechain	97.0 % (548 of 565)	98.0 % (343 of 350)	95.1 % (193 of 203)	100.0 % (12 of 12)
Aromatic	76.7 % (46 of 60)	86.7 % (26 of 30)	65.5 % (19 of 29)	100.0 % (1 of 1)
Methyl	100.0 % (68 of 68)	100.0 % (34 of 34)	100.0 % (34 of 34)

1. MSP1

GVDPKHVCVD TRDIPKNAGC FRDDDGTEEW RCLLGYKKGE GNTCVENNNP TCDINNGGCD PTASCQNAES TENSKKIICT CKEPTPNAYY EGVFCSSSS

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Temperature 273 K, Details 1mM 13C/15N pYoelii MSP1 25mM KPi 50mM Kcl ph6.5

#	Name	Isotope labeling	Type	Concentration
1	MSP1	[U-99% 13C; U-99% 15N]		1.0 mM
2	potassium chloride	natural abundance		50.0 mM
3	potassium phosphate	natural abundance		25.0 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: -0.18 ppm, Outliers: 9 Detail

LACS Plot; CB

Referencing offset: -0.18 ppm, Outliers: 9 Detail

LACS Plot; HA

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.54 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2015-09-01

Citation

The structure of Plasmodium yoelii merozoite surface protein 119, antibody specificity and implications for malaria vaccine design
Curd, R.D., Birdsall, B., Kadekoppala, M., Ogun, S.A., Kelly, G., Holder, A.A.
Open Biol. (2014), 4, 130091-130091, PubMed 24403012 , DOI 10.1098/rsob.130091 , Abstract

Related entities 1. msp1, : 1 : 2 : 31 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 273 K, Details 1mM 13C/15N pYoelii MSP1 25mM KPi 50mM Kcl ph6.5

#	Name	Isotope labeling	Type	Concentration
1	MSP1	[U-99% 13C; U-99% 15N]		1.0 mM
2	potassium chloride	natural abundance		50.0 mM
3	potassium phosphate	natural abundance		25.0 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 273 K, Details 1mM 13C/15N pYoelii MSP1 25mM KPi 50mM Kcl ph6.5

#	Name	Isotope labeling	Type	Concentration
1	MSP1	[U-99% 13C; U-99% 15N]		1.0 mM
2	potassium chloride	natural abundance		50.0 mM
3	potassium phosphate	natural abundance		25.0 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

3 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 273 K, Details 1mM 13C/15N pYoelii MSP1 25mM KPi 50mM Kcl ph6.5

#	Name	Isotope labeling	Type	Concentration
1	MSP1	[U-99% 13C; U-99% 15N]		1.0 mM
2	potassium chloride	natural abundance		50.0 mM
3	potassium phosphate	natural abundance		25.0 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

4 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 273 K, Details 1mM 13C/15N pYoelii MSP1 25mM KPi 50mM Kcl ph6.5

#	Name	Isotope labeling	Type	Concentration
1	MSP1	[U-99% 13C; U-99% 15N]		1.0 mM
2	potassium chloride	natural abundance		50.0 mM
3	potassium phosphate	natural abundance		25.0 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 273 K, Details 1mM 13C/15N pYoelii MSP1 25mM KPi 50mM Kcl ph6.5

#	Name	Isotope labeling	Type	Concentration
1	MSP1	[U-99% 13C; U-99% 15N]		1.0 mM
2	potassium chloride	natural abundance		50.0 mM
3	potassium phosphate	natural abundance		25.0 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 273 K, Details 1mM 13C/15N pYoelii MSP1 25mM KPi 50mM Kcl ph6.5

#	Name	Isotope labeling	Type	Concentration
1	MSP1	[U-99% 13C; U-99% 15N]		1.0 mM
2	potassium chloride	natural abundance		50.0 mM
3	potassium phosphate	natural abundance		25.0 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

7 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 273 K, Details 1mM 13C/15N pYoelii MSP1 25mM KPi 50mM Kcl ph6.5

#	Name	Isotope labeling	Type	Concentration
1	MSP1	[U-99% 13C; U-99% 15N]		1.0 mM
2	potassium chloride	natural abundance		50.0 mM
3	potassium phosphate	natural abundance		25.0 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

8 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 273 K, Details 1mM 13C/15N pYoelii MSP1 25mM KPi 50mM Kcl ph6.5

#	Name	Isotope labeling	Type	Concentration
1	MSP1	[U-99% 13C; U-99% 15N]		1.0 mM
2	potassium chloride	natural abundance		50.0 mM
3	potassium phosphate	natural abundance		25.0 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

9 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 273 K, Details 1mM 13C/15N pYoelii MSP1 25mM KPi 50mM Kcl ph6.5

#	Name	Isotope labeling	Type	Concentration
1	MSP1	[U-99% 13C; U-99% 15N]		1.0 mM
2	potassium chloride	natural abundance		50.0 mM
3	potassium phosphate	natural abundance		25.0 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19233_2mgp.nef
Input source #2: Coordindates	2mgp.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:8:CYS:SG	A:20:CYS:SG	oxidized, CA 56.55, CB 41.75 ppm	oxidized, CA 55.675, CB 41.317 ppm	2.037
A:32:CYS:SG	A:44:CYS:SG	oxidized, CA 54.261, CB 36.372 ppm	oxidized, CA 54.753, CB 42.023 ppm	2.023
A:52:CYS:SG	A:65:CYS:SG	oxidized, CA 55.998, CB 36.852 ppm	oxidized, CA 55.814, CB 37.995 ppm	2.034
A:59:CYS:SG	A:79:CYS:SG	oxidized, CA 52.856, CB 37.201 ppm	oxidized, CA 52.048, CB 39.167 ppm	2.026
A:81:CYS:SG	A:95:CYS:SG	oxidized, CA 55.78, CB 37.42 ppm	oxidized, CA 52.555, CB 40.953 ppm	2.042

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---------
GVDPKHVCVDTRDIPKNAGCFRDDDGTEEWRCLLGYKKGEGNTCVENNNPTCDINNGGCDPTASCQNAESTENSKKIICTCKEPTPNAYYEGVFCSSSS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GVDPKHVCVDTRDIPKNAGCFRDDDGTEEWRCLLGYKKGEGNTCVENNNPTCDINNGGCDPTASCQNAESTENSKKIICTCKEPTPNAYYEGVFCSSSS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	99	0	0	100.0

Content subtype: combined_19233_2mgp.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_chem_shift_list_1	Warning	1046		100.0 (chain: A, length: 99)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2191 (1)	noe	100.0 (chain: A, length: 99)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 556
  - ¹³C chemical shifts: 382
  - ¹⁵N chemical shifts: 108
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 100.0%
- Total number of restraints: 2188
- Weight of restraints: 1.0 (2188)
- Potential type of restraints: square-well-parabolic (2188)
- Range of distance target values: 1.53, 4.31 (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