BMRBj - BMREntryMaster

Found 1 Document (0.412 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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.412 seconds)

BMRB: 19759

Sample #1

Sample #2

Experiments performed 7 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail