BMRBj - BMREntryMaster

Found 1 Document (0.543 seconds)

BMRB: 30165

5T56

[3]catenane from MccJ25 G12R/I13C/G21C lasso peptide

Authors

Link, A.J., Allen, C.D.

Assembly

Microcin J25

Entity

1. Microcin J25 (polymer, Thiol state: not present), 12 monomers, 1288.410 × 2 Da Detail

GGAGHVPEYF VR

2. Microcin J25 (polymer, Thiol state: all disulfide bound), 9 monomers, 990.1538 × 2 Da Detail

CGTPISFYC

Total weight

4557.128 Da

Max. entity weight

1288.41 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	2:CYS1:SG	2:CYS9:SG

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.2 %, Completeness: 88.0 %, Completeness (bb): 81.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	88.0 % (103 of 117)	88.0 % (103 of 117)
Backbone	81.8 % (36 of 44)	81.8 % (36 of 44)
Sidechain	91.8 % (67 of 73)	91.8 % (67 of 73)
Aromatic	85.0 % (17 of 20)	85.0 % (17 of 20)
Methyl	100.0 % (8 of 8)	100.0 % (8 of 8)

1. Microcin J25

GGAGHVPEYF VR

2. Microcin J25

CGTPISFYC

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 295 K, Details 3.7 mg/mL [3]catenane from MccJ25 RCC lasso peptide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	[3]catenane from MccJ25 RCC lasso peptide	natural abundance	3.7 mg/mL
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

Protein Blocks Logo

Calculated from 20 models in PDB: 5T56, Strand ID: A, B, C, D Detail

Release date

2016-11-27

Citation

Self-Assembly of Catenanes from Lasso Peptides
Link, A.J., Allen, C.D.
J. Am. Chem. Soc. (2016), 138, 14214-14217, PubMed 27768305 , DOI 10.1021/jacs.6b09454 , Abstract

Related entities 1. Microcin J25, : 1 entities Detail

Experiments performed 2 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30165_5t56.nef
Input source #2: Coordindates	5t56.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)
B:13:CYS:SG	D:42:CYS:SG	unknown	unknown	2.038
B:21:CYS:SG	D:34:CYS:SG	unknown	unknown	2.038

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:GLY:N	1:8:GLU:CD	unknown	unknown	n/a
2:1:GLY:N	2:8:GLU:CD	unknown	unknown	n/a

Non-standard residues

None

Sequence alignments

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

--------10--
GGAGHVPEYFVR
||||||||||||
GGAGHVPEYFVR

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

------20-
CGTPISFYC
|||||||||
CGTPISFYC
---------

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

-------30---
GGAGHVPEYFVR
||||||||||||
GGAGHVPEYFVR
--------10--

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

-----40--
CGTPISFYC
|||||||||
CGTPISFYC
---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	12	100.0
B	B	9	100.0
C	C	12	100.0
D	D	9	100.0

Content subtype: combined_30165_5t56.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_chemical_shifts_1	Warning	206		100.0 (chain: A, length: 12), 88.9 (chain: B, length: 9), 100.0 (chain: C, length: 12), 88.9 (chain: D, length: 9)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1152 (1)	noe	100.0 (chain: A, length: 12), 88.9 (chain: B, length: 9), 58.3 (chain: C, length: 12), 88.9 (chain: D, length: 9)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 88.9%
  - Entity_assembly_ID: C, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: D, Chain length: 9, Sequence coverage: 88.9%
- Total number of assignments
  - ¹H chemical shifts: 206
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
  - Entity_assemble_ID: C
  - Entity_assemble_ID: D
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	61	91.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	22	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	39	95.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	9	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	42	84.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	14	77.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	28	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	3	3	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	8	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	61	91.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	22	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	39	95.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	9	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	42	84.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	14	77.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	28	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	3	3	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	8	88.9

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 88.9%
  - Entity_assembly_ID: C, Chain length: 12, Sequence coverage: 58.3%
  - Entity_assembly_ID: D, Chain length: 9, Sequence coverage: 88.9%
- Total number of restraints: 1150
- Weight of restraints: 1.0 (1150)
- Potential type of restraints: upper-bound-parabolic (1150)
- Range of distance target values: 2.4, 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
  - Chain_ID: C
  - Chain_ID: D
- Distance restraints on contact map

Keywords Catenane, Lasso Peptide

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Found 1 Document (0.543 seconds)

BMRB: 30165

Sample

Related entities 1. Microcin J25, : 1 entities Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail