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BMRB: 19489

2MDK

NMR SOLUTION STRUCTURE OF MSP-P56S DOMAIN/VAPB in DPC

Authors

Qin, H., Lim, L., Song, J.

Assembly

MSP-P56S DOMAIN/VAPB

Entity

1. MSP-P56S DOMAIN/VAPB (polymer), 125 monomers, 14187.16 Da Detail

MAKVEQVLSL EPQHELKFRG PFTDVVTTNL KLGNPTDRNV CFKVKTTAPR RYCVRSNSGI IDAGASINVS VMLQPFDYDP NEKSKHKFMV QSMFAPTDTS DMEAVWKEAK PEDLMDSKLR CVFEL

Formula weight

14187.16 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.6 %, Completeness: 60.0 %, Completeness (bb): 79.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	60.0 % (885 of 1476)	68.1 % (526 of 772)	41.7 % (240 of 576)	93.0 % (119 of 128)
Backbone	79.2 % (581 of 734)	94.3 % (232 of 246)	63.9 % (237 of 371)	95.7 % (112 of 117)
Sidechain	48.4 % (418 of 863)	55.9 % (294 of 526)	35.9 % (117 of 326)	63.6 % (7 of 11)
Aromatic	0.9 % (1 of 106)	1.9 % (1 of 53)	0.0 % (0 of 52)	0.0 % (0 of 1)
Methyl	43.7 % (55 of 126)	76.2 % (48 of 63)	11.1 % (7 of 63)

1. entity

MAKVEQVLSL EPQHELKFRG PFTDVVTTNL KLGNPTDRNV CFKVKTTAPR RYCVRSNSGI IDAGASINVS VMLQPFDYDP NEKSKHKFMV QSMFAPTDTS DMEAVWKEAK PEDLMDSKLR CVFEL

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 4

#	Name	Isotope labeling	Type	Concentration
1	MSP-P56S DOMAIN/VAPB	[U-13C; U-15N]		0.0 ~ 0.0 mM
2	DPC	natural abundance		20 mM

LACS Plot; CA

Referencing offset: 0.39 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.39 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.09 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2MDK, Strand ID: A Detail

Release date

2013-10-17

Citation

ALS-causing P56S mutation and splicing variation on the hVAPB MSP domain transform its β-sandwich fold into lipid-interacting helical conformations
Qin, H., Wang, W., Song, J.
Biochem. Biophys. Res. Commun. (2013), 431, 398-403, PubMed 23333387 , DOI 10.1016/j.bbrc.2013.01.039 , Abstract

Related entities 1. MSP-P56S DOMAIN/VAPB, : 1 : 5 : 75 entities Detail

Interaction partners 1. MSP-P56S DOMAIN/VAPB, : 53 interactors Detail

More details for 53 interactors identified by 25 citations

Experiments performed 9 experiments Detail

1 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 4

#	Name	Isotope labeling	Type	Concentration
1	MSP-P56S DOMAIN/VAPB	[U-13C; U-15N]		0.0 ~ 0.0 mM
2	DPC	natural abundance		20 mM

2 3D 1H-15N TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 4

#	Name	Isotope labeling	Type	Concentration
1	MSP-P56S DOMAIN/VAPB	[U-13C; U-15N]		0.0 ~ 0.0 mM
2	DPC	natural abundance		20 mM

3 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 4

#	Name	Isotope labeling	Type	Concentration
1	MSP-P56S DOMAIN/VAPB	[U-13C; U-15N]		0.0 ~ 0.0 mM
2	DPC	natural abundance		20 mM

4 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 4

#	Name	Isotope labeling	Type	Concentration
1	MSP-P56S DOMAIN/VAPB	[U-13C; U-15N]		0.0 ~ 0.0 mM
2	DPC	natural abundance		20 mM

5 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 4

#	Name	Isotope labeling	Type	Concentration
1	MSP-P56S DOMAIN/VAPB	[U-13C; U-15N]		0.0 ~ 0.0 mM
2	DPC	natural abundance		20 mM

6 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 4

#	Name	Isotope labeling	Type	Concentration
1	MSP-P56S DOMAIN/VAPB	[U-13C; U-15N]		0.0 ~ 0.0 mM
2	DPC	natural abundance		20 mM

7 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 4

#	Name	Isotope labeling	Type	Concentration
1	MSP-P56S DOMAIN/VAPB	[U-13C; U-15N]		0.0 ~ 0.0 mM
2	DPC	natural abundance		20 mM

8 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 4

#	Name	Isotope labeling	Type	Concentration
1	MSP-P56S DOMAIN/VAPB	[U-13C; U-15N]		0.0 ~ 0.0 mM
2	DPC	natural abundance		20 mM

9 3D C(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 4

#	Name	Isotope labeling	Type	Concentration
1	MSP-P56S DOMAIN/VAPB	[U-13C; U-15N]		0.0 ~ 0.0 mM
2	DPC	natural abundance		20 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19489_2mdk.nef
Input source #2: Coordindates	2mdk.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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRSNSGIIDAGASINVSVMLQPFDYDPNEKSKHKFMVQSMFAPTDTS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRSNSGIIDAGASINVSVMLQPFDYDPNEKSKHKFMVQSMFAPTDTS

-------110-------120-----
DMEAVWKEAKPEDLMDSKLRCVFEL
|||||||||||||||||||||||||
DMEAVWKEAKPEDLMDSKLRCVFEL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	125	0	0	100.0

Content subtype: combined_19489_2mdk.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	870		96.8 (chain: A, length: 125)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	483 (1)	noe	95.2 (chain: A, length: 125)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	688 (1)	pre	80.0 (chain: A, length: 125)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	117 (117)	.	64.0 (chain: A, length: 125)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 96.8%
- Total number of assignments
  - ¹³C chemical shifts: 230
  - ¹H chemical shifts: 522
  - ¹⁵N chemical shifts: 118
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 95.2%
- Total number of restraints: 483
- Weight of restraints: 1.0 (483)
- Potential type of restraints: square-well-parabolic (483)
- Range of distance target values: 2.8, 4.5 (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_4
  - Status: OK
  - Experiment type: pre
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 80.0%
  - Total number of restraints: 688
  - Weight of restraints: 1.0 (688)
  - Potential type of restraints: square-well-parabolic (688)
  - Range of distance target values: 10.0, 27.08 (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: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 64.0%
- Total number of restraints: 117
- Total number of restraints per polymer type: 117
- Weight of restraints: 1.0 (117)
- Potential type of restraints: square-well-parabolic (117)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords MSP-P56S DOMAIN, VAPB