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BMRB: 34520

6Z41

NMR solution structure of the carbohydrate-binding module family 73 (CBM73) from Cellvibrio japonicus CjLPMO10A

Authors

Madland, E., Aachmann, F.L., Courtade, G.

Assembly

Carbohydrate binding protein, putative, cpb33A

Entity

1. Carbohydrate binding protein, putative, cpb33A (polymer, Thiol state: all disulfide bound), 68 monomers, 7396.074 Da Detail

MGNCISPVYV DGSSYANNAL VQNNGSEYRC LVGGWCTVGG PYAPGTGWAW ANAWELVRSC QAHHHHHH

Formula weight

7396.074 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS60:SG
2	disulfide	sing	1:CYS30:SG	1:CYS36:SG

Source organism

Cellvibrio japonicus Ueda107

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.2 %, Completeness: 74.3 %, Completeness (bb): 87.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.3 % (547 of 736)	73.1 % (272 of 372)	72.6 % (207 of 285)	86.1 % (68 of 79)
Backbone	87.6 % (352 of 402)	88.0 % (125 of 142)	87.2 % (170 of 195)	87.7 % (57 of 65)
Sidechain	62.8 % (247 of 393)	63.9 % (147 of 230)	59.7 % (89 of 149)	78.6 % (11 of 14)
Aromatic	7.7 % (8 of 104)	7.7 % (4 of 52)	0.0 % (0 of 48)	100.0 % (4 of 4)
Methyl	100.0 % (58 of 58)	100.0 % (29 of 29)	100.0 % (29 of 29)

1. entity 1

MGNCISPVYV DGSSYANNAL VQNNGSEYRC LVGGWCTVGG PYAPGTGWAW ANAWELVRSC QAHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.1 mM CBM73, 25 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	CBM73	natural abundance	0.1 (±0.05) mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	10 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.1 mM CBM73, 25 mM sodium phosphate, 10 mM sodium chloride, 100% D2O

#	Name	Isotope labeling	Concentration
4	CBM73	natural abundance	0.1 (±0.05) mM
5	sodium phosphate	natural abundance	25 mM
6	sodium chloride	natural abundance	10 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.1 mM [U-15N] CBM73, 25 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	CBM73	[U-15N]	0.1 (±0.05) mM
8	sodium phosphate	natural abundance	25 mM
9	sodium chloride	natural abundance	10 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.1 mM [U-13C; U-15N] CBM73, 25 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
10	CBM73	[U-13C; U-15N]	0.1 (±0.05) mM
11	sodium phosphate	natural abundance	25 mM
12	sodium chloride	natural abundance	10 mM

Release date

2020-06-16

Citation

Structural and functional variation of chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus
Madland, E., Forsberg, Z., Wang, Y., Lindorff-Larsen, K., Niebisch, A., Modregger, J., Eijsink, V.G.H., Aachmann, F.L., Courtade, G.
J. Biol. Chem. (2021), 297, 101084-101084, PubMed 34411561 , DOI 10.1016/j.jbc.2021.101084 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 34519 released on 2020-07-13
Title NMR solution structure of the carbohydrate-binding module family 5 (CBM5) from Cellvibrio japonicus CjLPMO10A

Related entities 1. Carbohydrate binding protein, putative, cpb33A, : 1 : 4 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.1 mM CBM73, 25 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	CBM73	natural abundance	0.1 (±0.05) mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	10 mM

2 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - na MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.1 mM CBM73, 25 mM sodium phosphate, 10 mM sodium chloride, 100% D2O

#	Name	Isotope labeling	Concentration
4	CBM73	natural abundance	0.1 (±0.05) mM
5	sodium phosphate	natural abundance	25 mM
6	sodium chloride	natural abundance	10 mM

3 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.1 mM [U-15N] CBM73, 25 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	CBM73	[U-15N]	0.1 (±0.05) mM
8	sodium phosphate	natural abundance	25 mM
9	sodium chloride	natural abundance	10 mM

4 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.1 mM [U-13C; U-15N] CBM73, 25 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
10	CBM73	[U-13C; U-15N]	0.1 (±0.05) mM
11	sodium phosphate	natural abundance	25 mM
12	sodium chloride	natural abundance	10 mM

5 3D 1H-15N NOESY

Instrument

Bruker AVANCE III - na MHz

Sample

#	Name	Isotope labeling	Concentration
7	CBM73	[U-15N]	0.1 (±0.05) mM
8	sodium phosphate	natural abundance	25 mM
9	sodium chloride	natural abundance	10 mM

6 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - na MHz

Sample

#	Name	Isotope labeling	Concentration
10	CBM73	[U-13C; U-15N]	0.1 (±0.05) mM
11	sodium phosphate	natural abundance	25 mM
12	sodium chloride	natural abundance	10 mM

7 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.1 mM CBM73, 25 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	CBM73	natural abundance	0.1 (±0.05) mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	10 mM

8 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - na MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 0.1 mM CBM73, 25 mM sodium phosphate, 10 mM sodium chloride, 100% D2O

#	Name	Isotope labeling	Concentration
4	CBM73	natural abundance	0.1 (±0.05) mM
5	sodium phosphate	natural abundance	25 mM
6	sodium chloride	natural abundance	10 mM

9 3D HNCA

Instrument

Bruker AVANCE III - na MHz

Sample

#	Name	Isotope labeling	Concentration
10	CBM73	[U-13C; U-15N]	0.1 (±0.05) mM
11	sodium phosphate	natural abundance	25 mM
12	sodium chloride	natural abundance	10 mM

10 3D HCCH-TOCSY

Instrument

Bruker AVANCE III - na MHz

Sample

#	Name	Isotope labeling	Concentration
10	CBM73	[U-13C; U-15N]	0.1 (±0.05) mM
11	sodium phosphate	natural abundance	25 mM
12	sodium chloride	natural abundance	10 mM

11 3D 1H-13C NOESY

Instrument

Bruker AVANCE III - na MHz

Sample

#	Name	Isotope labeling	Concentration
10	CBM73	[U-13C; U-15N]	0.1 (±0.05) mM
11	sodium phosphate	natural abundance	25 mM
12	sodium chloride	natural abundance	10 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34520_3.str
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	None
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)
1:4:CYS:SG	1:60:CYS:SG	oxidized, CA 54.8, CB 44.0 ppm	oxidized, CA 54.5, CB 41.4 ppm	n/a
1:30:CYS:SG	1:36:CYS:SG	oxidized, CA 58.2, CB 41.3 ppm	oxidized, CA 58.5, CB 44.5 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr34520_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	600		89.7 (chain: 1, length: 68)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 68, Sequence coverage: 89.7%
- Total number of assignments
  - ¹H chemical shifts: 327
  - ¹³C chemical shifts: 206
  - ¹⁵N chemical shifts: 67
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	372	269	72.3
¹³C chemical shifts	285	206	72.3
¹⁵N chemical shifts	79	67	84.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	142	122	85.9
¹³C chemical shifts	136	117	86.0
¹⁵N chemical shifts	65	56	86.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	230	147	63.9
¹³C chemical shifts	149	89	59.7
¹⁵N chemical shifts	14	11	78.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	29	96.7
¹³C chemical shifts	30	29	96.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	4	7.7
¹³C chemical shifts	48	0	0.0
¹⁵N chemical shifts	4	4	100.0

Keywords SUGAR BINDING PROTEIN, cbm, chitin

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Found 1 Document (0.524 seconds)

BMRB: 34520

Sample #1

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Sample #4

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Carbohydrate binding protein, putative, cpb33A, : 1 : 4 entities Detail

Experiments performed 11 experiments Detail

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Chemical shift validation 3 contents Detail