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Found 1 Document (0.588 seconds)

BMRB: 30475

6DMZ

Solution structure of ZmD32

Authors

Harvey, P.J., Craik, D.J.

Assembly

Flower-specific gamma-thionin

Entity

1. Flower-specific gamma-thionin (polymer, Thiol state: all disulfide bound), 47 monomers, 5466.252 Da Detail

RTCQSQSHRF RGPCLRRSNC ANVCRTEGFP GGRCRGFRRR CFCTTHC

Formula weight

5466.252 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS47:SG
2	disulfide	sing	1:CYS14:SG	1:CYS34:SG
3	disulfide	sing	1:CYS20:SG	1:CYS41:SG
4	disulfide	sing	1:CYS24:SG	1:CYS43:SG

Source organism

Zea mays

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.9 %, Completeness: 74.8 %, Completeness (bb): 72.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.8 % (398 of 532)	89.8 % (256 of 285)	53.0 % (105 of 198)	75.5 % (37 of 49)
Backbone	72.3 % (201 of 278)	92.8 % (90 of 97)	57.4 % (78 of 136)	73.3 % (33 of 45)
Sidechain	79.1 % (234 of 296)	88.3 % (166 of 188)	61.5 % (64 of 104)	100.0 % (4 of 4)
Aromatic	45.8 % (22 of 48)	70.8 % (17 of 24)	20.8 % (5 of 24)
Methyl	100.0 % (18 of 18)	100.0 % (9 of 9)	100.0 % (9 of 9)

1. entity 1

RTCQSQSHRF RGPCLRRSNC ANVCRTEGFP GGRCRGFRRR CFCTTHC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 3.5, Details 1 mM peptide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	peptide	natural abundance		1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 3.5, Details 1 mM peptide, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	peptide	natural abundance		1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6DMZ, Strand ID: A Detail

Release date

2018-07-26

Citation

Salt-Tolerant Antifungal and Antibacterial Activities of the Corn Defensin ZmD32
Kerenga, B.K., McKenna, J.A., Harvey, P.J., Quimbar, P., Garcia-Ceron, D., Lay, F.T., Phan, T.K., Veneer, P.K., Vasa, S., Parisi, K., Shafee, T., van der Weerden, N.L., Hulett, M.D., Craik, D.J., Anderson, M.A., Bleackley, M.R.
Front. Microbiol. (2019), 10, 795-795, PubMed 31031739 , DOI 10.3389/fmicb.2019.00795 , Abstract

Related entities 1. Flower-specific gamma-thionin, : 1 : 1 : 133 entities Detail

Experiments performed 7 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30475_6dmz.nef
Input source #2: Coordindates	6dmz.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:47:CYS:SG	oxidized, CA 57.978, CB 43.232 ppm	oxidized, CB 42.614 ppm	2.016
A:14:CYS:SG	A:34:CYS:SG	unknown, CA 57.464 ppm	oxidized, CA 52.179, CB 36.644 ppm	2.041
A:20:CYS:SG	A:41:CYS:SG	oxidized, CB 35.955 ppm	oxidized, CA 60.137, CB 35.741 ppm	2.02
A:24:CYS:SG	A:43:CYS:SG	oxidized, CB 38.291 ppm	oxidized, CA 51.687, CB 35.799 ppm	2.034

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-------
RTCQSQSHRFRGPCLRRSNCANVCRTEGFPGGRCRGFRRRCFCTTHC
|||||||||||||||||||||||||||||||||||||||||||||||
RTCQSQSHRFRGPCLRRSNCANVCRTEGFPGGRCRGFRRRCFCTTHC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	47	0	0	100.0

Content subtype: combined_30475_6dmz.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	397		97.9 (chain: A, length: 47)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	740 (1)	noe	93.6 (chain: A, length: 47)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	24 (1)	hbond	38.3 (chain: A, length: 47)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	74 (74)	.	97.9 (chain: A, length: 47)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 97.9%
- Total number of assignments
  - ¹H chemical shifts: 261
  - ¹³C chemical shifts: 99
  - ¹⁵N chemical shifts: 37
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	285	261	91.6
¹³C chemical shifts	198	99	50.0
¹⁵N chemical shifts	60	37	61.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	97	92	94.8
¹³C chemical shifts	94	40	42.6
¹⁵N chemical shifts	45	33	73.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	188	169	89.9
¹³C chemical shifts	104	59	56.7
¹⁵N chemical shifts	15	4	26.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	9	100.0
¹³C chemical shifts	9	9	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	18	75.0
¹³C chemical shifts	24	0	0.0

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: 47, Sequence coverage: 93.6%
- Total number of restraints: 740
- Weight of restraints: 1.0 (740)
- Potential type of restraints: square-well-parabolic (740)
- Range of distance target values: 2.28, 3.65 (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_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 38.3%
  - Total number of restraints: 24
  - Weight of restraints: 1.0 (24)
  - Potential type of restraints: square-well-parabolic (24)
  - Range of distance target values: 1.0, 1.5 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 97.9%
- Total number of restraints: 74
- Total number of restraints per polymer type: 74
- Weight of restraints: 1.0 (74)
- Potential type of restraints: square-well-parabolic (74)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ANTIFUNGAL PROTEIN, antimicrobial peptide, plant defensin

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Found 1 Document (0.588 seconds)

BMRB: 30475

Sample #1

Sample #2

Related entities 1. Flower-specific gamma-thionin, : 1 : 1 : 133 entities Detail

Experiments performed 7 experiments Detail

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NMR combined restraints 5 contents Detail