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BMRB: 25725

2N5Q

Solution structure of cystein-rich peptide jS1 from Jasminum sambac

Authors

Shin, J., Kumari, G., Serra, A., Nguyen, P.Q.T., Yoon, H., Tam, J.P.

Assembly

cystein-rich peptide jS1

Entity

1. cystein-rich peptide jS1 (polymer, Thiol state: all disulfide bound), 27 monomers, 3129.664 Da Detail

QLCLQCRSNS DCNIIWRICR DGCCNVI

Formula weight

3129.664 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS23:SG
2	disulfide	sing	1:CYS6:SG	1:CYS19:SG
3	disulfide	sing	1:CYS12:SG	1:CYS24:SG

Source organism

Jasminum sambac

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.8 %, Completeness (bb): 92.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	93.8 % (151 of 161)	93.8 % (151 of 161)
Backbone	92.7 % (51 of 55)	92.7 % (51 of 55)
Sidechain	94.3 % (100 of 106)	94.3 % (100 of 106)
Aromatic	100.0 % (6 of 6)	100.0 % (6 of 6)
Methyl	100.0 % (14 of 14)	100.0 % (14 of 14)

1. entity

QLCLQCRSNS DCNIIWRICR DGCCNVI

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	jS1	natural abundance	protein	0.7 ~ 1.0 mM
2	H2O	natural abundance	solvent	90 %
3	D2O	[U-2H]	solvent	10 %
4	sodium phosphate	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	50 mM
6	sodium azide	natural abundance		0.01 % w/v

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	jS1	natural abundance	protein	0.7 ~ 1.0 mM
8	D2O	[U-2H]	solvent	100 %
9	sodium phosphate	natural abundance	buffer	20 mM
10	sodium chloride	natural abundance	salt	50 mM
11	sodium azide	natural abundance		0.01 % w/v

Protein Blocks Logo

Calculated from 20 models in PDB: 2N5Q, Strand ID: A Detail

Release date

2016-07-24

Citation

Cysteine-Rich Peptide Family with Unusual Disulfide Connectivity from Jasminum sambac
Kumari, G., Serra, A., Shin, J., Nguyen, P.Q.T., Sze, S., Yoon, H., Tam, J.P.
J. Nat. Prod. (2015), 78, 2791-2799, PubMed 26555361 , DOI 10.1021/acs.jnatprod.5b00762 , Abstract

Related entities 1. cystein-rich peptide jS1, : 4 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25725_2n5q.nef
Input source #2: Coordindates	2n5q.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:3:CYS:SG	A:23:CYS:SG	unknown	unknown	2.031
A:6:CYS:SG	A:19:CYS:SG	unknown	unknown	2.03
A:12:CYS:SG	A:24:CYS:SG	unknown	unknown	2.03

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

--------10--------20-------
QLCLQCRSNSDCNIIWRICRDGCCNVI
|||||||||||||||||||||||||||
QLCLQCRSNSDCNIIWRICRDGCCNVI

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	27	0	0	100.0

Content subtype: combined_25725_2n5q.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	151		100.0 (chain: A, length: 27)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1078 (1)	noe	100.0 (chain: A, length: 27)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	10 (1)	hbond	29.6 (chain: A, length: 27)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	22 (22)	.	96.3 (chain: A, length: 27)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 151
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	161	151	93.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	55	51	92.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	106	100	94.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	14	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0

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: 27, Sequence coverage: 100.0%
- Total number of restraints: 1077
- Weight of restraints: 1.0 (1077)
- Potential type of restraints: square-well-parabolic (1077)
- Range of distance target values: 2.4, 4.4 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 29.6%
  - Total number of restraints: 10
  - Weight of restraints: 1.0 (10)
  - Potential type of restraints: square-well-parabolic (10)
  - Range of distance target values: 1.9, 2.4 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - 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: 27, Sequence coverage: 96.3%
- Total number of restraints: 22
- Total number of restraints per polymer type: 22
- Weight of restraints: 1.0 (22)
- Potential type of restraints: square-well-parabolic (22)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords cystein-rich peptide

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Found 1 Document (0.56 seconds)

BMRB: 25725

Sample #1

Sample #2

Related entities 1. cystein-rich peptide jS1, : 4 entities Detail

Experiments performed 5 experiments Detail

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Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail