BMRBj - BMREntryMaster

Found 1 Document (0.574 seconds)

BMRB: 25332

2MWK

Family 1 Carbohydrate-Binding Module from Trichoderma reesei Cel7A with O-mannose residues at Thr1, Ser3, and Ser14

Authors

Happs, R.M., Chen, L., Resch, M.G., Davis, M.F., Beckham, G.T., Tan, Z., Crowley, M.F.

Assembly

Family 1 Carbohydrate-Binding Module from Trichoderma reesei Cel7A with O-mannose residues at Thr1, Ser3, and Ser14

Entity

1. CBM 3M (polymer), 36 monomers, 3745.115 Da Detail

TQSHYGQCGG IGYSGPTVCA SGTTCQVLNP YYSQCL

2. ALPHA-D-MANNOSE (non-polymer), 180.156 × 3 Da

Total weight

4285.583 Da

Max. entity weight

3745.115 Da

Source organism

Trichoderma reesei

Exptl. method

solution NMR

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete1

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

Polymer type: polypeptide(L)

	Total	¹H
All	100.0 % (190 of 190)	100.0 % (190 of 190)
Backbone	100.0 % (76 of 76)	100.0 % (76 of 76)
Sidechain	100.0 % (114 of 114)	100.0 % (114 of 114)
Aromatic	100.0 % (18 of 18)	100.0 % (18 of 18)
Methyl	100.0 % (15 of 15)	100.0 % (15 of 15)

1. CBM 3M

TQSHYGQCGG IGYSGPTVCA SGTTCQVLNP YYSQCL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5

#	Name	Isotope labeling	Concentration
1	CBM_3M	natural abundance	1.5 mg
2	D2O	natural abundance	10 %
3	H2O	natural abundance	90 %
4	NaCl	natural abundance	30 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 5

#	Name	Isotope labeling	Concentration
5	CBM_3M	natural abundance	1.5 mg
6	D2O	natural abundance	100 %
7	NaCl	natural abundance	30 mM

Chem. Shift Complete2

Sequence coverage: 5.6 %, Completeness: 50.5 %, Completeness (bb): 51.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	50.5 % (192 of 380)	50.5 % (192 of 380)
Backbone	51.3 % (78 of 152)	51.3 % (78 of 152)
Sidechain	50.0 % (114 of 228)	50.0 % (114 of 228)
Aromatic	50.0 % (18 of 36)	50.0 % (18 of 36)
Methyl	50.0 % (15 of 30)	50.0 % (15 of 30)

1. CBM 3M

TQSHYGQCGG IGYSGPTVCA SGTTCQVLNP YYSQCL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5

#	Name	Isotope labeling	Concentration
1	CBM_3M	natural abundance	1.5 mg
2	D2O	natural abundance	10 %
3	H2O	natural abundance	90 %
4	NaCl	natural abundance	30 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 5

#	Name	Isotope labeling	Concentration
5	CBM_3M	natural abundance	1.5 mg
6	D2O	natural abundance	100 %
7	NaCl	natural abundance	30 mM

Protein Blocks Logo

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

Release date

2015-08-30

Citation

O-glycosylation effects on family 1 carbohydrate-binding module solution structures
Happs, R.M., Chen, L., Resch, M.G., Davis, M.F., Beckham, G.T., Tan, Z., Crowley, M.F.
FEBS J. (2015), 282, 4341-4356, PubMed 26307003 , DOI 10.1111/febs.13500 , Abstract

Related entities 1. CBM 3M, : 1 : 10 : 1 : 9 : 100 entities Detail

Experiments performed 6 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25332_2mwk.nef
Input source #2: Coordindates	2mwk.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:8:CYS:SG	A:25:CYS:SG	unknown	unknown	2.036
A:19:CYS:SG	A:35:CYS:SG	unknown	unknown	2.016

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:THR:CB	2:1:MAN:O1	unknown	unknown	n/a
1:3:SER:CB	2:2:MAN:O1	unknown	unknown	n/a
1:14:SER:CB	2:3:MAN:O1	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	MAN	alpha-D-mannopyranose	Assigned chemical shifts
B	2	MAN	alpha-D-mannopyranose	Assigned chemical shifts
B	3	MAN	alpha-D-mannopyranose	Assigned chemical shifts

Sequence alignments

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

--------10--------20--------30------
TQSHYGQCGGIGYSGPTVCASGTTCQVLNPYYSQCL
||||||||||||||||||||||||||||||||||||
TQSHYGQCGGIGYSGPTVCASGTTCQVLNPYYSQCL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	36	0	0	100.0

Content subtype: combined_25332_2mwk.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	190		100.0 (chain: A, length: 36)
2	Assigned chemical shifts	assigned_chem_shift_list_2	Warning	6		100.0 (chain: B, length: 3)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	514 (1)	noe	100.0 (chain: A, length: 36)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	20 (1)	hbond	38.9 (chain: A, length: 36)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	22	.	86.1 (chain: A, length: 36)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 190
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
Saveframe: assigned_chem_shift_list_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 3, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 6
- Completeness of assignments
  - Entity_assemble_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
13	TYR	HH	9.178

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	190	189	99.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	75	98.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	114	114	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	15	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	18	100.0

Comp_index_ID	Comp_ID
1	MAN
2	MAN
3	MAN

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 100.0%
- Total number of restraints: 514
- Weight of restraints: 1.0 (514)
- Potential type of restraints: square-well-parabolic (514)
- Range of distance target values: 2.15, 3.65 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- 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: 36, Sequence coverage: 38.9%
  - Total number of restraints: 20
  - Weight of restraints: 1.0 (20)
  - Potential type of restraints: square-well-parabolic (20)
  - Range of distance target values: 2.0, 2.85 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - 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: 36, Sequence coverage: 86.1%

Keywords NMR, O-glycosylation, carbohydrate-binding module

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Found 1 Document (0.574 seconds)

BMRB: 25332

Sample #1

Sample #2

Sample #1

Sample #2

Related entities 1. CBM 3M, : 1 : 10 : 1 : 9 : 100 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail