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Found 1 Document (0.556 seconds)

BMRB: 36142

5YZ6

Solution structure of LysM domain from a chitinase derived from Volvox carteri

Authors

Kitaoku, Y., Nishimura, S., Fukamizo, T., Ohnuma, T.

Assembly

Chitinase, lysozyme

Entity

1. Chitinase, lysozyme (polymer, Thiol state: all disulfide bound), 49 monomers, 5302.070 Da Detail

MGCTYTIQPG DTFWAIAQRR GTTVDVIQSL NPGVVPTRLQ VGQVINVPC

Formula weight

5302.07 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS49:SG

Source organism

Volvox carteri f. nagariensis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.4 %, Completeness (bb): 99.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.4 % (531 of 551)	94.7 % (268 of 283)	98.1 % (211 of 215)	98.1 % (52 of 53)
Backbone	99.0 % (283 of 286)	98.0 % (97 of 99)	100.0 % (142 of 142)	97.8 % (44 of 45)
Sidechain	94.5 % (292 of 309)	92.9 % (171 of 184)	96.6 % (113 of 117)	100.0 % (8 of 8)
Aromatic	73.3 % (22 of 30)	73.3 % (11 of 15)	71.4 % (10 of 14)	100.0 % (1 of 1)
Methyl	100.0 % (68 of 68)	100.0 % (34 of 34)	100.0 % (34 of 34)

1. entity 1

MGCTYTIQPG DTFWAIAQRR GTTVDVIQSL NPGVVPTRLQ VGQVINVPC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 189 K, pH 5.0, Details 360 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	LysM	[U-13C; U-15N]	protein	360 uM
2	sodium acetate	[U-2H]	buffer	20 mM
3	H2O	natural abundance	solvent	90 %
4	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 189 K, pH 5.0, Details 267 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	LysM	[U-13C; U-15N]	protein	267 uM
6	sodium acetate	[U-2H]	buffer	20 mM
7	D2O	[U-2H]	solvent	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	14.7 ppm	internal	indirect	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	36.5 ppm	internal	indirect	0.1013291

Referencing offset: 2.9 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	14.7 ppm	internal	indirect	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	36.5 ppm	internal	indirect	0.1013291

Referencing offset: 2.9 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	14.7 ppm	internal	indirect	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	36.5 ppm	internal	indirect	0.1013291

Referencing offset: 0.11 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	14.7 ppm	internal	indirect	0.2514495
¹H	water	protons	4.7 ppm	internal	direct	1.0
¹⁵N	water	protons	36.5 ppm	internal	indirect	0.1013291

Referencing offset: 2.67 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5YZ6, Strand ID: A Detail

Release date

2018-06-18

Citation

Structures and chitin-binding properties of two N-terminal lysin motifs (LysMs) found in a chitinase from Volvox carteri
Kitaoku, Y., Nishimura, S., Hirono, T., Suginta, W., Ohnuma, T., Fukamizo, T.
Glycobiology (2019), 29, 565-575, PubMed 30976779 , DOI 10.1093/glycob/cwz024 , Abstract

Related entities 1. Chitinase, lysozyme, : 1 : 2 : 141 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 189 K, pH 5.0, Details 267 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	LysM	[U-13C; U-15N]	protein	267 uM
6	sodium acetate	[U-2H]	buffer	20 mM
7	D2O	[U-2H]	solvent	100 %

2 3D HNCO

Instrument

Bruker AvanceIII - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 189 K, pH 5.0, Details 267 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	LysM	[U-13C; U-15N]	protein	267 uM
6	sodium acetate	[U-2H]	buffer	20 mM
7	D2O	[U-2H]	solvent	100 %

3 3D HNCACO

Instrument

Bruker AvanceIII - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 189 K, pH 5.0, Details 267 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	LysM	[U-13C; U-15N]	protein	267 uM
6	sodium acetate	[U-2H]	buffer	20 mM
7	D2O	[U-2H]	solvent	100 %

4 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 189 K, pH 5.0, Details 267 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	LysM	[U-13C; U-15N]	protein	267 uM
6	sodium acetate	[U-2H]	buffer	20 mM
7	D2O	[U-2H]	solvent	100 %

5 3D HNCACB

Instrument

Bruker AvanceIII - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 189 K, pH 5.0, Details 267 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	LysM	[U-13C; U-15N]	protein	267 uM
6	sodium acetate	[U-2H]	buffer	20 mM
7	D2O	[U-2H]	solvent	100 %

6 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.0, Details 360 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	LysM	[U-13C; U-15N]	protein	360 uM
2	sodium acetate	[U-2H]	buffer	20 mM
3	H2O	natural abundance	solvent	90 %
4	D2O	[U-2H]	solvent	10 %

7 3D HBHACBCACONH

Instrument

Bruker AvanceIII - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 189 K, pH 5.0, Details 267 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	LysM	[U-13C; U-15N]	protein	267 uM
6	sodium acetate	[U-2H]	buffer	20 mM
7	D2O	[U-2H]	solvent	100 %

8 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 189 K, pH 5.0, Details 267 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	LysM	[U-13C; U-15N]	protein	267 uM
6	sodium acetate	[U-2H]	buffer	20 mM
7	D2O	[U-2H]	solvent	100 %

9 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.0, Details 360 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	LysM	[U-13C; U-15N]	protein	360 uM
2	sodium acetate	[U-2H]	buffer	20 mM
3	H2O	natural abundance	solvent	90 %
4	D2O	[U-2H]	solvent	10 %

10 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.0, Details 360 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	LysM	[U-13C; U-15N]	protein	360 uM
2	sodium acetate	[U-2H]	buffer	20 mM
3	H2O	natural abundance	solvent	90 %
4	D2O	[U-2H]	solvent	10 %

11 3D CCH-TOCSY

Instrument

Bruker AvanceIII - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5.0, Details 360 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	LysM	[U-13C; U-15N]	protein	360 uM
2	sodium acetate	[U-2H]	buffer	20 mM
3	H2O	natural abundance	solvent	90 %
4	D2O	[U-2H]	solvent	10 %

12 3D 1H-15N TOCSY

Instrument

Bruker AvanceIII - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 189 K, pH 5.0, Details 267 uM [U-13C; U-15N] LysM, 20 mM [U-2H] sodium acetate, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	LysM	[U-13C; U-15N]	protein	267 uM
6	sodium acetate	[U-2H]	buffer	20 mM
7	D2O	[U-2H]	solvent	100 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_36142_5yz6.nef
Input source #2: Coordindates	5yz6.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	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)
A:21:CYS:SG	A:67:CYS:SG	oxidized, CA 56.324, CB 42.753 ppm	oxidized, CA 52.979, CB 38.992 ppm	2.008

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

None

Non-standard residues

None

Sequence alignments

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

-20-------30--------40--------50--------60-------
MGCTYTIQPGDTFWAIAQRRGTTVDVIQSLNPGVVPTRLQVGQVINVPC
|||||||||||||||||||||||||||||||||||||||||||||||||
MGCTYTIQPGDTFWAIAQRRGTTVDVIQSLNPGVVPTRLQVGQVINVPC
--------10--------20--------30--------40---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	49	0	0	100.0

Content subtype: combined_36142_5yz6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	534		100.0 (chain: A, length: 49)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	10 (1)	undefined	6.1 (chain: A, length: 49)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	10 (1)	undefined	6.1 (chain: A, length: 49)
3	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	42 (1)	hbond	55.1 (chain: A, length: 49)
4	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	42 (1)	hbond	55.1 (chain: A, length: 49)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	21 (21)	.	32.7 (chain: A, length: 49)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 49, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 269
  - ¹³C chemical shifts: 210
  - ¹⁵N chemical shifts: 55
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
30	THR	HG1	5.594
40	THR	HG1	6.296

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	283	267	94.3
¹³C chemical shifts	215	210	97.7
¹⁵N chemical shifts	56	55	98.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	99	97	98.0
¹³C chemical shifts	98	98	100.0
¹⁵N chemical shifts	45	44	97.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	184	170	92.4
¹³C chemical shifts	117	112	95.7
¹⁵N chemical shifts	11	11	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	34	97.1
¹³C chemical shifts	35	34	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	11	73.3
¹³C chemical shifts	14	10	71.4
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 49, Sequence coverage: 6.1%
- Total number of restraints: 10
- Weight of restraints: 1.0 (10)
- Potential type of restraints: upper-bound-parabolic (10)
- Range of distance target values: 1.51, 3.1 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_5
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 49, Sequence coverage: 6.1%
  - Total number of restraints: 10
  - Weight of restraints: 1.0 (10)
  - Potential type of restraints: upper-bound-parabolic (10)
  - Range of distance target values: 1.49, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_4
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 49, Sequence coverage: 55.1%
    - Total number of restraints: 42
    - Weight of restraints: 1.0 (42)
    - Potential type of restraints: upper-bound-parabolic (42)
    - Range of distance target values: 2.0, 3.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_6
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 49, Sequence coverage: 55.1%
        -20-------30--------40--------50--------60------- MGCTYTIQPGDTFWAIAQRRGTTVDVIQSLNPGVVPTRLQVGQVINVPC | | || |||| ||| | |||||||||| || ||| ..C.Y.IQ..DTFW.IAQ.R.TTVDVIQSLN..........GQ.INV -20-------30--------40--------50--------60-----
      - Total number of restraints: 42
        Total hydrogen bond restraints: 42
        O...H-x (too close!): 13
        O...h-N (too close!): 13
        Long range: 16
        O...H-x (too close!): 8
        O...h-N (too close!): 8
      - Weight of restraints: 1.0 (42)
        Total hydrogen bond restraints: 1.0 (42)
        O...H-x (too close!): 1.0 (13)
        O...h-N (too close!): 1.0 (13)
        Long range: 1.0 (16)
        O...H-x (too close!): 1.0 (8)
        O...h-N (too close!): 1.0 (8)
      - Potential type of restraints: upper-bound-parabolic (42)
        Total hydrogen bond restraints: upper-bound-parabolic (42)
        O...H-x (too close!): upper-bound-parabolic (13)
        O...h-N (too close!): upper-bound-parabolic (13)
        Long range: upper-bound-parabolic (16)
        O...H-x (too close!): upper-bound-parabolic (8)
        O...h-N (too close!): upper-bound-parabolic (8)
      - Range of distance target values: 1.8, 2.7 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 49, Sequence coverage: 32.7%
- Total number of restraints: 21
- Total number of restraints per polymer type: 21
- Weight of restraints: 1.0 (21)
- Potential type of restraints: square-well-parabolic (21)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords CBM50, HYDROLASE, SUGAR BINDING PROTEIN, chitin-specific, lysin motif

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Found 1 Document (0.556 seconds)

BMRB: 36142

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Chitinase, lysozyme, : 1 : 2 : 141 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 7 contents Detail