BMRBj - BMREntryMaster

Found 1 Document (0.768 seconds)

BMRB: 15737

2K33

Solution structure of an N-glycosylated protein using in vitro glycosylation

Authors

Slynko, V., Schubert, M., Numao, S., Kowarik, M., Aebi, M., Allain, F.H.-T.

Assembly

AcrA(61-210DD) glycosylated

Entity

1. AcrA (61-210DD) (polymer, Thiol state: not present), 116 monomers, 12729.09 Da Detail

DVIIKPQVSG VIVNKLFKAG DKVKKGQTLF IIEQDQASKD FNRSKALFSQ SAISQKEYDS SLATLDHTEI KAPFDGTIGD ALVNIGDYVS ASTTELVRVT NLNPIYADGS HHHHHH

2. SUGAR (7-MER) (polymer, Thiol state: not present), 7 monomers, 1196.129 Da

Total weight

13925.219 Da

Max. entity weight

12729.09 Da

Entity Connection

covalent 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	covalent	sing	1:ASN42:ND2	2:X1:C1

Source organism

Campylobacter jejuni

Exptl. method

solution NMR

Refine. method

distance geometry

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.1 %, Completeness: 80.6 %, Completeness (bb): 79.4 % Detail

Polymer type: polypeptide(L) polysaccharide(D)

	Total	¹H	¹³C	¹⁵N
All	80.6 % (1071 of 1328)	88.6 % (605 of 683)	67.0 % (349 of 521)	94.4 % (117 of 124)
Backbone	79.4 % (548 of 690)	91.9 % (217 of 236)	66.0 % (225 of 341)	93.8 % (106 of 113)
Sidechain	83.8 % (626 of 747)	86.8 % (388 of 447)	78.5 % (227 of 289)	100.0 % (11 of 11)
Aromatic	33.3 % (34 of 102)	62.7 % (32 of 51)	3.9 % (2 of 51)
Methyl	95.0 % (133 of 140)	91.4 % (64 of 70)	98.6 % (69 of 70)

1. AcrA (61-210DD)

DVIIKPQVSG VIVNKLFKAG DKVKKGQTLF IIEQDQASKD FNRSKALFSQ SAISQKEYDS SLATLDHTEI KAPFDGTIGD ALVNIGDYVS ASTTELVRVT NLNPIYADGS HHHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 15N sample H2O

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 15N]	1 mM
2	SUGAR (7-MER)	natural abundance	1 mM
3	potassium phosphate	natural abundance	50 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 13C/15N sample H2O

#	Name	Isotope labeling	Concentration
4	entity_1	[U-100% 13C; U-100% 15N]	1 mM
5	SUGAR (7-MER)	natural abundance	1 mM
6	potassium phosphate	natural abundance	50 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 15N sample D2O

#	Name	Isotope labeling	Concentration
7	entity_1	[U-100% 15N]	1 mM
8	SUGAR (7-MER)	natural abundance	1 mM
9	potassium phosphate	natural abundance	50 mM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 13C/15N sample D2O

#	Name	Isotope labeling	Concentration
10	entity_1	[U-100% 13C; U-100% 15N]	1 mM
11	SUGAR (7-MER)	natural abundance	1 mM
12	potassium phosphate	natural abundance	50 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2K33, Strand ID: A Detail

Release date

2009-01-22

Citation

NMR structure determination of a segmentally labeled glycoprotein using in vitro glycosylation
Slynko, V., Schubert, M., Numao, S., Kowarik, M., Aebi, M., Allain, F.H.-T.
J. Am. Chem. Soc. (2009), 131, 1274-1281, PubMed 19154179 , DOI 10.1021/ja808682v , Abstract

Related entities 1. AcrA (61-210DD), : 1 : 1 : 69 entities Detail

Experiments performed 17 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 15N sample H2O

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 15N]	1 mM
2	SUGAR (7-MER)	natural abundance	1 mM
3	potassium phosphate	natural abundance	50 mM

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 15N sample D2O

#	Name	Isotope labeling	Concentration
7	entity_1	[U-100% 15N]	1 mM
8	SUGAR (7-MER)	natural abundance	1 mM
9	potassium phosphate	natural abundance	50 mM

3 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 13C/15N sample H2O

#	Name	Isotope labeling	Concentration
4	entity_1	[U-100% 13C; U-100% 15N]	1 mM
5	SUGAR (7-MER)	natural abundance	1 mM
6	potassium phosphate	natural abundance	50 mM

4 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 15N sample H2O

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 15N]	1 mM
2	SUGAR (7-MER)	natural abundance	1 mM
3	potassium phosphate	natural abundance	50 mM

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 15N sample H2O

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 15N]	1 mM
2	SUGAR (7-MER)	natural abundance	1 mM
3	potassium phosphate	natural abundance	50 mM

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 15N sample D2O

#	Name	Isotope labeling	Concentration
7	entity_1	[U-100% 15N]	1 mM
8	SUGAR (7-MER)	natural abundance	1 mM
9	potassium phosphate	natural abundance	50 mM

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 13C/15N sample H2O

#	Name	Isotope labeling	Concentration
4	entity_1	[U-100% 13C; U-100% 15N]	1 mM
5	SUGAR (7-MER)	natural abundance	1 mM
6	potassium phosphate	natural abundance	50 mM

8 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 13C/15N sample H2O

#	Name	Isotope labeling	Concentration
4	entity_1	[U-100% 13C; U-100% 15N]	1 mM
5	SUGAR (7-MER)	natural abundance	1 mM
6	potassium phosphate	natural abundance	50 mM

9 3D HN(CO)CA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 13C/15N sample H2O

#	Name	Isotope labeling	Concentration
4	entity_1	[U-100% 13C; U-100% 15N]	1 mM
5	SUGAR (7-MER)	natural abundance	1 mM
6	potassium phosphate	natural abundance	50 mM

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 13C/15N sample D2O

#	Name	Isotope labeling	Concentration
10	entity_1	[U-100% 13C; U-100% 15N]	1 mM
11	SUGAR (7-MER)	natural abundance	1 mM
12	potassium phosphate	natural abundance	50 mM

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 13C/15N sample H2O

#	Name	Isotope labeling	Concentration
4	entity_1	[U-100% 13C; U-100% 15N]	1 mM
5	SUGAR (7-MER)	natural abundance	1 mM
6	potassium phosphate	natural abundance	50 mM

12 3D 1H-15N NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 15N sample H2O

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 15N]	1 mM
2	SUGAR (7-MER)	natural abundance	1 mM
3	potassium phosphate	natural abundance	50 mM

13 2D 13C filtered-filtered NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 13C/15N sample D2O

#	Name	Isotope labeling	Concentration
10	entity_1	[U-100% 13C; U-100% 15N]	1 mM
11	SUGAR (7-MER)	natural abundance	1 mM
12	potassium phosphate	natural abundance	50 mM

14 2D 15N filtered-filtered NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 15N sample H2O

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 15N]	1 mM
2	SUGAR (7-MER)	natural abundance	1 mM
3	potassium phosphate	natural abundance	50 mM

15 3D 13C edited-filtered NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 13C/15N sample D2O

#	Name	Isotope labeling	Concentration
10	entity_1	[U-100% 13C; U-100% 15N]	1 mM
11	SUGAR (7-MER)	natural abundance	1 mM
12	potassium phosphate	natural abundance	50 mM

16 2D 13C filtered-edited NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 13C/15N sample D2O

#	Name	Isotope labeling	Concentration
10	entity_1	[U-100% 13C; U-100% 15N]	1 mM
11	SUGAR (7-MER)	natural abundance	1 mM
12	potassium phosphate	natural abundance	50 mM

17 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 13C/15N sample D2O

#	Name	Isotope labeling	Concentration
10	entity_1	[U-100% 13C; U-100% 15N]	1 mM
11	SUGAR (7-MER)	natural abundance	1 mM
12	potassium phosphate	natural abundance	50 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15737_2k33.nef
Input source #2: Coordindates	2k33.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	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	B6D	2,4-bisacetamido-2,4,6-trideoxy-beta-D-glucopyranose	Coordinates
B	2	A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	Coordinates
B	3	A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	Coordinates
B	4	A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	Coordinates
B	5	A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	Coordinates
B	6	A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	Coordinates
B	7	BGC	beta-D-glucopyranose	Coordinates

Sequence alignments

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

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

-------110------
NLNPIYADGSHHHHHH
||||||||||||||||
NLNPIYADGSHHHHHH

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

-------
XXXXXXX
|||||||
XXXXXXX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	116	0	0	100.0
B	B	7	0	0	100.0

Content subtype: combined_15737_2k33.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	1188		No information
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1932 (1)	noe	92.2 (chain: A, length: 116)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	2 (1)	noe	No information
3	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	52 (1)	hbond	28.4 (chain: A, length: 116)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 92.2%
- Total number of restraints: 1932
- Weight of restraints: 1.0 (1932)
- Potential type of restraints: upper-bound-parabolic (1932)
- Range of distance target values: 2.57, 5.8 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: OK
  - Experiment type: noe
  - Total number of restraints: 2
  - Weight of restraints: 1.0 (2)
  - Potential type of restraints: upper-bound-parabolic (2)
  - Range of distance target values: 4.6, 4.6 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_5
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 28.4%
    - Total number of restraints: 52
    - Weight of restraints: 1.0 (52)
    - Potential type of restraints: upper-bound-parabolic (52)
    - Range of distance target values: 2.3, 3.2 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map

Keywords glycoprotein, glycosylation, N-glycan

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Found 1 Document (0.768 seconds)

BMRB: 15737

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Related entities 1. AcrA (61-210DD), : 1 : 1 : 69 entities Detail

Experiments performed 17 experiments Detail

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NMR combined restraints 5 contents Detail