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BMRB: 19878

2MN3

Structure of Platypus 'Intermediate' Defensin-like Peptide (Int-DLP)

Authors

Torres, A.M., Bansal, P.S., Koh, J.MS., Pages, G., Wu, M.J., Kuchel, P.W.

Assembly

Int-DLP

Entity

1. Int-DLP (polymer, Thiol state: all disulfide bound), 44 monomers, 4988.801 Da Detail

RRRRRRPPCE DVNGQCQPRG NPCLRLRGAC PRGSRCCMPT VAAH

Formula weight

4988.801 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS9:SG	1:CYS36:SG
2	disulfide	sing	1:CYS16:SG	1:CYS30:SG
3	disulfide	sing	1:CYS23:SG	1:CYS37:SG

Source organism

Ornithorhynchus anatinus

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.7 %, Completeness: 73.2 %, Completeness (bb): 90.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	73.2 % (197 of 269)	73.2 % (197 of 269)
Backbone	90.7 % (78 of 86)	90.7 % (78 of 86)
Sidechain	65.0 % (119 of 183)	65.0 % (119 of 183)
Aromatic	100.0 % (2 of 2)	100.0 % (2 of 2)
Methyl	83.3 % (10 of 12)	83.3 % (10 of 12)

1. Int-DLP

RRRRRRPPCE DVNGQCQPRG NPCLRLRGAC PRGSRCCMPT VAAH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.5, Details chemically synthesized Int-DLP

#	Name	Isotope labeling	Type	Concentration
1	Int-DLP	natural abundance		1.0 ~ 2.0 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2MN3, Strand ID: A Detail

Release date

2014-09-14

Citation 1

Structure and antimicrobial activity of platypus 'intermediate' defensin-like peptide
Torres, A.M., Bansal, P.S., Koh, J.MS., Pages, G., Wu, M.J., Kuchel, P.W.
FEBS Lett. (2014), 588, 1821-1826, PubMed 24694388 , DOI 10.1016/j.febslet.2014.03.044 , Abstract

Show more 1 citaion

Citation 2

Defensins and the convergent evolution of platypus and reptile venom genes
Whittington, C.M., Papenfuss, A.T., Bansal, P., Torres, A.M., Wong, E.SW., Deakin, J.E., Graves, T., Alsop, A., Schatzkamer, K., Kremitzki, C., Ponting, C.P., Temple-Smith, P., Warren, W.C., Kuchel, P.W., Katherine, B.
Genome Res. (2008), 18, 986-994, PubMed 18463304 , DOI 10.1101/gr.7149808 , Abstract

Hide non-primary 1 citaion

Related entities 1. Int-DLP, : 1 : 1 : 1 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19878_2mn3.nef
Input source #2: Coordindates	2mn3.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:9:CYS:SG	A:36:CYS:SG	unknown	unknown	2.117
A:16:CYS:SG	A:30:CYS:SG	unknown	unknown	1.957
A:23:CYS:SG	A:37:CYS:SG	unknown	unknown	2.11

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--------30--------40----
RRRRRRPPCEDVNGQCQPRGNPCLRLRGACPRGSRCCMPTVAAH
||||||||||||||||||||||||||||||||||||||||||||
RRRRRRPPCEDVNGQCQPRGNPCLRLRGACPRGSRCCMPTVAAH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	44	0	0	100.0

Content subtype: combined_19878_2mn3.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	196		97.7 (chain: A, length: 44)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	562 (1)	noe	88.6 (chain: A, length: 44)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	9 (1)	undefined	13.6 (chain: A, length: 44)
3	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	9 (1)	undefined	13.6 (chain: A, length: 44)
4	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	24 (1)	hbond	38.6 (chain: A, length: 44)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 97.7%
- Total number of assignments
  - ¹H chemical shifts: 196
- 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	269	196	72.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	86	78	90.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	183	118	64.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	10	76.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	2	100.0

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: 44, Sequence coverage: 88.6%
- Total number of restraints: 562
- Weight of restraints: 1.0 (562)
- Potential type of restraints: upper-bound-parabolic (562)
- 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
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 13.6%
  - Total number of restraints: 9
  - Weight of restraints: 1.0 (9)
  - Potential type of restraints: upper-bound-parabolic (9)
  - Range of distance target values: 2.1, 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: 44, Sequence coverage: 13.6%
    - Total number of restraints: 9
    - Weight of restraints: 1.0 (9)
    - Potential type of restraints: upper-bound-parabolic (9)
    - 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_4
      - Status: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 44, Sequence coverage: 38.6%
      - Total number of restraints: 24
        Total hydrogen bond restraints: 24
        O...H-x: 4
        O...h-N: 4
        Long range: 16
        O...H-x: 8
        O...h-N: 8
      - Weight of restraints: 1.0 (24)
        Total hydrogen bond restraints: 1.0 (24)
        O...H-x: 1.0 (4)
        O...h-N: 1.0 (4)
        Long range: 1.0 (16)
        O...H-x: 1.0 (8)
        O...h-N: 1.0 (8)
      - Potential type of restraints: upper-bound-parabolic (24)
        Total hydrogen bond restraints: upper-bound-parabolic (24)
        O...H-x: upper-bound-parabolic (4)
        O...h-N: upper-bound-parabolic (4)
        Long range: upper-bound-parabolic (16)
        O...H-x: upper-bound-parabolic (8)
        O...h-N: upper-bound-parabolic (8)
      - Range of distance target values: 2.2, 3.2 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map

Keywords defensin-like peptide, platypus defensin, beta-defensin, intermediate-DLP

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Found 1 Document (0.591 seconds)

BMRB: 19878

Sample

Related entities 1. Int-DLP, : 1 : 1 : 1 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail