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BMRB: 25404

2MXD

Solution structure of VPg of porcine sapovirus

Authors

Kim, J., Hwang, H., Min, H., Yun, H., Cho, K., Pelton, J.G., Wemmer, D.E., Lee, C.

Assembly

VPg of porcine sapovirus

Entity

1. VPg of porcine sapovirus (polymer, Thiol state: not present), 62 monomers, 7372.146 Da Detail

GAMAIALRDD EYDEWQDIIR DWRKEMTVQQ FLDLKERALS GASDPDSQRY NAWLELRAKR LS

Formula weight

7372.146 Da

Source organism

Porcine epidemic diarrhea virus

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.2 %, Completeness (bb): 98.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.2 % (722 of 743)	96.4 % (377 of 391)	98.2 % (278 of 283)	97.1 % (67 of 69)
Backbone	98.6 % (365 of 370)	99.2 % (124 of 125)	98.9 % (182 of 184)	96.7 % (59 of 61)
Sidechain	96.3 % (417 of 433)	95.1 % (253 of 266)	98.1 % (156 of 159)	100.0 % (8 of 8)
Aromatic	90.3 % (56 of 62)	90.3 % (28 of 31)	89.3 % (25 of 28)	100.0 % (3 of 3)
Methyl	100.0 % (60 of 60)	100.0 % (30 of 30)	100.0 % (30 of 30)

1. entity

GAMAIALRDD EYDEWQDIIR DWRKEMTVQQ FLDLKERALS GASDPDSQRY NAWLELRAKR LS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.6 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.6 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.08 ppm, Outliers: 4 Detail

LACS Plot; CO

Referencing offset: -0.49 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2015-04-12

Citation

Solution structure of the porcine sapovirus VPg core reveals a stable three-helical bundle with a conserved surface patch
Hwang, H., Min, H., Yun, H., Pelton, J., Wemmer, D., Cho, K., Kim, J., Lee, C.
Biochem. Biophys. Res. Commun. (2015), 459, 610-616, PubMed 25753201 , DOI 10.1016/j.bbrc.2015.02.156 , Abstract

Related entities 1. VPg of porcine sapovirus, : 1 : 1 : 29 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 3D HNCO

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D HNCA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

7 3D HCCH-COSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

8 3D 1H-15N NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

9 3D 1H-15N TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25404_2mxd.nef
Input source #2: Coordindates	2mxd.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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

---950-------960-------970-------980-------990------1000------
GAMAIALRDDEYDEWQDIIRDWRKEMTVQQFLDLKERALSGASDPDSQRYNAWLELRAKRLS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMAIALRDDEYDEWQDIIRDWRKEMTVQQFLDLKERALSGASDPDSQRYNAWLELRAKRLS
--------10--------20--------30--------40--------50--------60--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	62	0	0	100.0

Content subtype: combined_25404_2mxd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	723		100.0 (chain: A, length: 62)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1287 (1)	noe	98.4 (chain: A, length: 62)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	58 (1)	hbond	66.1 (chain: A, length: 62)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	95 (95)	.	87.1 (chain: A, length: 62)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 379
  - ¹³C chemical shifts: 277
  - ¹⁵N chemical shifts: 67
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 98.4%
- Total number of restraints: 1284
- Weight of restraints: 1.0 (1284)
- Potential type of restraints: square-well-parabolic (1284)
- Range of distance target values: 1.13, 2.78 (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: 62, Sequence coverage: 66.1%
  - Total number of restraints: 58
  - Weight of restraints: 1.0 (58)
  - Potential type of restraints: square-well-parabolic (58)
  - Range of distance target values: 1.0, 1.5 (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: 62, Sequence coverage: 87.1%
- Total number of restraints: 95
- Total number of restraints per polymer type: 95
- Weight of restraints: 1.0 (95)
- Potential type of restraints: square-well-parabolic (95)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Porcine sapovirus, Viral protein genome-linked