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BMRB: 25269

2MVI

Structure of ASM1

Authors

Goroncy, A.K., Loo, T.S., Koolaard, A., Patchett, M.L., Norris, G.E.

Assembly

ASM1

Entity

1. ASM1, entity 1 (polymer), 43 monomers, 4646.164 Da Detail

KPAWCWYTLA MCGAGYDSGT CDYMYSHCFG VKHSSGGGGS YHC

2. N-ACETYL-D-GLUCOSAMINE (non-polymer), 221.208 × 2 Da

Total weight

5088.58 Da

Max. entity weight

4646.164 Da

Entity Connection

disulfide 2, covalent 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS5:SG	1:CYS28:SG
2	disulfide	sing	1:CYS12:SG	1:CYS21:SG
3	covalent	sing	1:CYS43:SG	2:NAG1:C1
4	covalent	sing	1:SER18:OG	2:NAG1:C1

Source organism

Lactiplantibacillus plantarum

Exptl. method

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.3 %, Completeness (bb): 81.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.3 % (401 of 454)	96.5 % (221 of 229)	75.7 % (137 of 181)	97.7 % (43 of 44)
Backbone	81.6 % (209 of 256)	96.8 % (90 of 93)	64.5 % (78 of 121)	97.6 % (41 of 42)
Sidechain	97.0 % (226 of 233)	96.3 % (131 of 136)	97.9 % (93 of 95)	100.0 % (2 of 2)
Aromatic	100.0 % (86 of 86)	100.0 % (43 of 43)	100.0 % (41 of 41)	100.0 % (2 of 2)
Methyl	88.9 % (16 of 18)	77.8 % (7 of 9)	100.0 % (9 of 9)

1. entity 1

KPAWCWYTLA MCGAGYDSGT CDYMYSHCFG VKHSSGGGGS YHC

Show sample condition

Sample

Solvent system 38% d3-acetonitrile, 56.8% water, 0.2% d-acetic acid, 5% D2O, Pressure 1 atm, Temperature 310 K

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		1 mM
2	d3-acetonitrile	natural abundance		38 %
3	water	natural abundance		56.8 %
4	d-acetic acid	natural abundance		0.2 %
5	D2O	natural abundance		5 %

Protein Blocks Logo

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

Release date

2014-10-07

Citation

Structural Characterization of the S-glycosylated Bacteriocin ASM1 from Lactobacillus plantarum
Goroncy, A.K., Loo, T.S., Koolaard, A., Patchett, M.L., Norris, G.E.
Magnetochemistry (2020), 6, 16-16, PubMed , DOI 10.3390/magnetochemistry6010016

Related entities 1. ASM1, entity 1, : 1 : 1 : 1 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz Equipped with cryoprobe (CPTCI 1H-13C/15N/D Z-GRD)

Sample

State isotropic, Solvent system 38% d3-acetonitrile, 56.8% water, 0.2% d-acetic acid, 5% D2O, Pressure 1 atm, Temperature 310 K

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		1 mM
2	d3-acetonitrile	natural abundance		38 %
3	water	natural abundance		56.8 %
4	d-acetic acid	natural abundance		0.2 %
5	D2O	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz Equipped with cryoprobe (CPTCI 1H-13C/15N/D Z-GRD)

Sample

State isotropic, Solvent system 38% d3-acetonitrile, 56.8% water, 0.2% d-acetic acid, 5% D2O, Pressure 1 atm, Temperature 310 K

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		1 mM
2	d3-acetonitrile	natural abundance		38 %
3	water	natural abundance		56.8 %
4	d-acetic acid	natural abundance		0.2 %
5	D2O	natural abundance		5 %

3 2D 1H-13C HMBC

Instrument

Bruker Avance - 700 MHz Equipped with cryoprobe (CPTCI 1H-13C/15N/D Z-GRD)

Sample

State isotropic, Solvent system 38% d3-acetonitrile, 56.8% water, 0.2% d-acetic acid, 5% D2O, Pressure 1 atm, Temperature 310 K

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		1 mM
2	d3-acetonitrile	natural abundance		38 %
3	water	natural abundance		56.8 %
4	d-acetic acid	natural abundance		0.2 %
5	D2O	natural abundance		5 %

4 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz Equipped with cryoprobe (CPTCI 1H-13C/15N/D Z-GRD)

Sample

State isotropic, Solvent system 38% d3-acetonitrile, 56.8% water, 0.2% d-acetic acid, 5% D2O, Pressure 1 atm, Temperature 310 K

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		1 mM
2	d3-acetonitrile	natural abundance		38 %
3	water	natural abundance		56.8 %
4	d-acetic acid	natural abundance		0.2 %
5	D2O	natural abundance		5 %

5 2D 1H-15N-HSQC-TOCSY

Instrument

Bruker Avance - 700 MHz Equipped with cryoprobe (CPTCI 1H-13C/15N/D Z-GRD)

Sample

State isotropic, Solvent system 38% d3-acetonitrile, 56.8% water, 0.2% d-acetic acid, 5% D2O, Pressure 1 atm, Temperature 310 K

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		1 mM
2	d3-acetonitrile	natural abundance		38 %
3	water	natural abundance		56.8 %
4	d-acetic acid	natural abundance		0.2 %
5	D2O	natural abundance		5 %

6 2D 1H-13C-HSQC-TOCSY

Instrument

Bruker Avance - 700 MHz Equipped with cryoprobe (CPTCI 1H-13C/15N/D Z-GRD)

Sample

State isotropic, Solvent system 38% d3-acetonitrile, 56.8% water, 0.2% d-acetic acid, 5% D2O, Pressure 1 atm, Temperature 310 K

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		1 mM
2	d3-acetonitrile	natural abundance		38 %
3	water	natural abundance		56.8 %
4	d-acetic acid	natural abundance		0.2 %
5	D2O	natural abundance		5 %

7 2D 1H-13C-H2BC

Instrument

Bruker Avance - 700 MHz Equipped with cryoprobe (CPTCI 1H-13C/15N/D Z-GRD)

Sample

State isotropic, Solvent system 38% d3-acetonitrile, 56.8% water, 0.2% d-acetic acid, 5% D2O, Pressure 1 atm, Temperature 310 K

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		1 mM
2	d3-acetonitrile	natural abundance		38 %
3	water	natural abundance		56.8 %
4	d-acetic acid	natural abundance		0.2 %
5	D2O	natural abundance		5 %

8 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz Equipped with cryoprobe (CPTCI 1H-13C/15N/D Z-GRD)

Sample

State isotropic, Solvent system 38% d3-acetonitrile, 56.8% water, 0.2% d-acetic acid, 5% D2O, Pressure 1 atm, Temperature 310 K

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		1 mM
2	d3-acetonitrile	natural abundance		38 %
3	water	natural abundance		56.8 %
4	d-acetic acid	natural abundance		0.2 %
5	D2O	natural abundance		5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25269_2mvi.nef
Input source #2: Coordindates	2mvi.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:5:CYS:SG	A:28:CYS:SG	oxidized, CA 55.113, CB 36.372 ppm	oxidized, CA 55.394, CB 39.479 ppm	2.077
A:12:CYS:SG	A:21:CYS:SG	oxidized, CA 55.551, CB 39.733 ppm	oxidized, CA 55.364, CB 38.016 ppm	1.985

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)
1:18:SER:OG	2:1:NAG:C1	unknown	unknown	n/a
1:43:CYS:SG	2:2:NAG:C1	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	Assigned chemical shifts, Distance restraints
B	2	NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	None

Sequence alignments

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

--------10--------20--------30--------40---
KPAWCWYTLAMCGAGYDSGTCDYMYSHCFGVKHSSGGGGSYHC
|||||||||||||||||||||||||||||||||||||||||||
KPAWCWYTLAMCGAGYDSGTCDYMYSHCFGVKHSSGGGGSYHC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	43	0	0	100.0

Content subtype: combined_25269_2mvi.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	437		100.0 (chain: A, length: 43), 50.0 (chain: B, length: 2)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	8 (1)	undefined	11.6 (chain: A, length: 43), 50.0 (chain: B, length: 2)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	657 (1)	noe	93.0 (chain: A, length: 43), 50.0 (chain: B, length: 2)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	33 (28)	.	72.1 (chain: A, length: 43)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 43, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 2, Sequence coverage: 50.0%
- Total number of assignments
  - ¹H chemical shifts: 248
  - ¹³C chemical shifts: 145
  - ¹⁵N chemical shifts: 44
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 43, Sequence coverage: 11.6%
  - Entity_assembly_ID: B, Chain length: 2, Sequence coverage: 50.0%
- Total number of restraints: 8
- Weight of restraints: 1.0 (8)
- Potential type of restraints: upper-bound-parabolic (8)
- Range of distance target values: 2.0, 3.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 43, Sequence coverage: 93.0%
    - Entity_assembly_ID: B, Chain length: 2, Sequence coverage: 50.0%
  - Total number of restraints: 657
  - Weight of restraints: 1.0 (657)
  - Potential type of restraints: upper-bound-parabolic (657)
  - Range of distance target values: 2.34, 5.5 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 43, Sequence coverage: 72.1%
- Total number of restraints: 28
- Total number of restraints per polymer type: 28
- Weight of restraints: 1.0 (28)
- Potential type of restraints: square-well-parabolic (28)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords O-glycosylation, S-glycosylation, antimicrobial peptide, bacteriocin, glycocin, glycopeptide, nmr