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Found 1 Document (0.378 seconds)

BMRB: 19759

2MK7

Tetra-O-GalNAc glycosylated mucin sequence from alpha dystroglycan mucin domain

Authors

Live, D., Borgert, A.

Assembly

Tetra-O-GalNAc glycosylated mucin sequence from alpha dystroglycan mucin domain

Entity

1. aDG Mucin Domain Peptide (polymer, Thiol state: not present), 11 monomers, 994.1633 Da Detail

XPPTTTTKKP X

2. SUGAR (4-MER) (polymer, Thiol state: not present), 4 monomers, 830.7862 Da

Total weight

1824.9495 Da

Max. entity weight

994.1633 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 60.0 %, Completeness: 91.5 %, Completeness (bb): 81.3 % Detail

Polymer type: polypeptide(L) polysaccharide(D)

	Total	¹H	¹³C	¹⁵N
All	91.5 % (97 of 106)	100.0 % (57 of 57)	79.1 % (34 of 43)	100.0 % (6 of 6)
Backbone	81.3 % (39 of 48)	100.0 % (15 of 15)	66.7 % (18 of 27)	100.0 % (6 of 6)
Sidechain	100.0 % (67 of 67)	100.0 % (42 of 42)	100.0 % (25 of 25)
Methyl	100.0 % (8 of 8)	100.0 % (4 of 4)	100.0 % (4 of 4)

1. aDG Mucin Domain Peptide

XPPTTTTKKP X

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	aDG_Mucin_Domain_Peptide	natural abundance		2.0 ~ 10.0 mM
2	D2O	natural abundance		100 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 4.5

#	Name	Isotope labeling	Concentration
3	aDG_Mucin_Domain_Peptide	natural abundance	2.0 ~ 10.0 mM
4	D2O	natural abundance	5 %
5	H2O	natural abundance	95 %

Protein Blocks Logo

Calculated from 16 models in PDB: 2MK7, Strand ID: A Detail

Release date

2015-02-01

Experiments performed 7 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19759_2mk7.nef
Input source #2: Coordindates	2mk7.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:1:ACE:C	1:2:PRO:N	unknown	unknown	n/a
1:4:THR:OG1	2:1:A2G:C1	unknown	unknown	n/a
1:5:THR:OG1	2:2:A2G:C1	unknown	unknown	n/a
1:6:THR:OG1	2:3:A2G:C1	unknown	unknown	n/a
1:7:THR:OG1	2:4:A2G:C1	unknown	unknown	n/a
1:10:PRO:C	1:11:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	ACE	ACETYL GROUP	Coordinates
A	11	NH2	AMINO GROUP	Coordinates
B	1	A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	Assigned chemical shifts
B	2	A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	Assigned chemical shifts
B	3	A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	Assigned chemical shifts
B	4	A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	Assigned chemical shifts

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10-
XPPTTTTKKPX
|||||||||||
XPPTTTTKKPX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	11	0	0	100.0

Content subtype: combined_19759_2mk7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	6		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	177		81.8 (chain: A, length: 11), 100.0 (chain: B, length: 4)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	51 (1)	noe	81.8 (chain: A, length: 11)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 81.8%
  - Entity_assembly_ID: B, Chain length: 4, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 105
  - ¹³C chemical shifts: 62
  - ¹⁵N chemical shifts: 10
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	57	93.4
¹³C chemical shifts	45	34	75.6
¹⁵N chemical shifts	7	6	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	15	93.8
¹³C chemical shifts	18	9	50.0
¹⁵N chemical shifts	7	6	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	42	93.3
¹³C chemical shifts	27	25	92.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	4	80.0
¹³C chemical shifts	5	4	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	36	100.0
¹³C chemical shifts	32	28	87.5
¹⁵N chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	28	100.0
¹³C chemical shifts	24	24	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	8	100.0
¹³C chemical shifts	8	4	50.0
¹⁵N chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	4	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 81.8%
- Total number of restraints: 51
- Weight of restraints: 1.0 (51)
- Potential type of restraints: square-well-parabolic (51)
- Range of distance target values: 2.4, 3.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Keywords alpha-dystroglycan, glycoprotein, glycosylation, mucin domain, N-acetyl-galactosamine, Tn antigen

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Found 1 Document (0.378 seconds)

BMRB: 19759

Sample #1

Sample #2

Experiments performed 7 experiments Detail

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NMR combined restraints 3 contents Detail