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BMRB: 19834

2MLW

New Cyt-like delta-endotoxins from Dickeya dadantii - CytC protein

Authors

Loth, K., Costechareyre, D., Effantin, G., Rahbe, Y., Contemine, G., Landon, C., Da Silva, P.

Assembly

New Cyt-like delta-endotoxins from Dickeya dadantii - CytC protein

Entity

1. New Cyt-like delta-endotoxins from Dickeya dadantii - CytC protein (polymer), 203 monomers, 22395.09 Da Detail

MSIEIYPDDG NTLPYQVFLN LENEHYYAQA IQLAQLFAHE VDDNGQLDLA KALKKAQAQP DLAIIATNNM TLKKSFSTLS ALTTTLSEQL KIEGVLGISQ DTYIQNILSH AFCDLETQKD KPWFHINAQP DAGHSVTSYS YSLFIVSQGE ETGAMMAAGP LIITVTPNTA ISDIFNTKDW RLTLQKEEIT IGVKGFQVVT PLG

Formula weight

22395.09 Da

Source organism

Dickeya dadantii

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 81.4 %, Completeness (bb): 95.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.4 % (1917 of 2354)	79.7 % (963 of 1208)	79.8 % (737 of 924)	97.7 % (217 of 222)
Backbone	95.6 % (1149 of 1202)	96.1 % (393 of 409)	94.3 % (564 of 598)	98.5 % (192 of 195)
Sidechain	70.4 % (946 of 1344)	71.3 % (570 of 799)	67.8 % (351 of 518)	92.6 % (25 of 27)
Aromatic	33.9 % (61 of 180)	57.8 % (52 of 90)	8.0 % (7 of 88)	100.0 % (2 of 2)
Methyl	78.4 % (207 of 264)	81.1 % (107 of 132)	75.8 % (100 of 132)

1. entity

MSIEIYPDDG NTLPYQVFLN LENEHYYAQA IQLAQLFAHE VDDNGQLDLA KALKKAQAQP DLAIIATNNM TLKKSFSTLS ALTTTLSEQL KIEGVLGISQ DTYIQNILSH AFCDLETQKD KPWFHINAQP DAGHSVTSYS YSLFIVSQGE ETGAMMAAGP LIITVTPNTA ISDIFNTKDW RLTLQKEEIT IGVKGFQVVT PLG

Show sample condition

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CytC	[U-13C; U-15N]		0.3 mM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		90 %
7	DTT	natural abundance		10 %

Protein Blocks Logo

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

Release date

2015-02-15

Citation

New Cyt-like δ-endotoxins from Dickeya dadantii: structure and aphicidal activity
Loth, K., Costechareyre, D., Effantin, G., Rahbe, Y., Contdemine, G., Landon, C., Da Silva, P.
Sci. Rep. (2015), 5, 8791-8791, PubMed 25740111 , DOI 10.1038/srep08791 , Abstract

Related entities 1. New Cyt-like delta-endotoxins from Dickeya dadantii - CytC protein, : 1 entities Detail

Experiments performed 12 experiments Detail

1 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CytC	[U-13C; U-15N]		0.3 mM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		90 %
7	DTT	natural abundance		10 %

2 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CytC	[U-13C; U-15N]		0.3 mM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		90 %
7	DTT	natural abundance		10 %

3 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CytC	[U-13C; U-15N]		0.3 mM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		90 %
7	DTT	natural abundance		10 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CytC	[U-13C; U-15N]		0.3 mM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		90 %
7	DTT	natural abundance		10 %

5 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CytC	[U-13C; U-15N]		0.3 mM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		90 %
7	DTT	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CytC	[U-13C; U-15N]		0.3 mM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		90 %
7	DTT	natural abundance		10 %

7 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CytC	[U-13C; U-15N]		0.3 mM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		90 %
7	DTT	natural abundance		10 %

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CytC	[U-13C; U-15N]		0.3 mM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		90 %
7	DTT	natural abundance		10 %

9 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CytC	[U-13C; U-15N]		0.3 mM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		90 %
7	DTT	natural abundance		10 %

10 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CytC	[U-13C; U-15N]		0.3 mM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		90 %
7	DTT	natural abundance		10 %

11 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CytC	[U-13C; U-15N]		0.3 mM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		90 %
7	DTT	natural abundance		10 %

12 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CytC	[U-13C; U-15N]		0.3 mM
2	TRIS	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	EDTA	natural abundance		1 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		90 %
7	DTT	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19834_2mlw.nef
Input source #2: Coordindates	2mlw.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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--------50--------60--------70--------80--------90-------100
MSIEIYPDDGNTLPYQVFLNLENEHYYAQAIQLAQLFAHEVDDNGQLDLAKALKKAQAQPDLAIIATNNMTLKKSFSTLSALTTTLSEQLKIEGVLGISQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSIEIYPDDGNTLPYQVFLNLENEHYYAQAIQLAQLFAHEVDDNGQLDLAKALKKAQAQPDLAIIATNNMTLKKSFSTLSALTTTLSEQLKIEGVLGISQ

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
DTYIQNILSHAFCDLETQKDKPWFHINAQPDAGHSVTSYSYSLFIVSQGEETGAMMAAGPLIITVTPNTAISDIFNTKDWRLTLQKEEITIGVKGFQVVT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
DTYIQNILSHAFCDLETQKDKPWFHINAQPDAGHSVTSYSYSLFIVSQGEETGAMMAAGPLIITVTPNTAISDIFNTKDWRLTLQKEEITIGVKGFQVVT

---
PLG
|||
PLG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	203	0	0	100.0

Content subtype: combined_19834_2mlw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1887		99.5 (chain: A, length: 203)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	4816 (1)	noe	97.5 (chain: A, length: 203)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	351 (351)	.	88.7 (chain: A, length: 203)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 203, Sequence coverage: 99.5%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MSIEIYPDDGNTLPYQVFLNLENEHYYAQAIQLAQLFAHEVDDNGQLDLAKALKKAQAQPDLAIIATNNMTLKKSFSTLSALTTTLSEQLKIEGVLGISQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSIEIYPDDGNTLPYQVFLNLENEHYYAQAIQLAQLFAHEVDDNGQLDLAKALKKAQAQPDLAIIATNNMTLKKSFSTLSALTTTLSEQLKIEGVLGISQ

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
DTYIQNILSHAFCDLETQKDKPWFHINAQPDAGHSVTSYSYSLFIVSQGEETGAMMAAGPLIITVTPNTAISDIFNTKDWRLTLQKEEITIGVKGFQVVT
||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
DTYIQNILSHAFCDLET.KDKPWFHINAQPDAGHSVTSYSYSLFIVSQGEETGAMMAAGPLIITVTPNTAISDIFNTKDWRLTLQKEEITIGVKGFQVVT

---
PLG
|||
PLG

Total number of assignments
- ¹H chemical shifts: 945
- ¹³C chemical shifts: 727
- ¹⁵N chemical shifts: 215

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	SER	HG	1.658
20	ASN	CG	179.365
23	ASN	CG	180.214
32	GLN	CD	180.186
35	GLN	CD	179.377
46	GLN	CD	180.131
51	LYS	HZ1	7.665
51	LYS	HZ2	7.665
51	LYS	HZ3	7.665
51	LYS	NZ	71.878
55	LYS	HZ1	7.282
55	LYS	HZ2	7.282
55	LYS	HZ3	7.282
57	GLN	CD	179.907
59	GLN	CD	179.583
69	ASN	CG	177.11
89	GLN	CD	177.132
105	GLN	CD	179.318
106	ASN	CG	180.35
129	GLN	CD	180.194
168	ASN	CG	176.865
178	LYS	HZ1	8.32
178	LYS	HZ2	8.32
178	LYS	HZ3	8.32
178	LYS	NZ	71.562

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1208	935	77.4
¹³C chemical shifts	924	714	77.3
¹⁵N chemical shifts	223	213	95.5

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	409	393	96.1
¹³C chemical shifts	406	382	94.1
¹⁵N chemical shifts	195	189	96.9

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	799	542	67.8
¹³C chemical shifts	518	332	64.1
¹⁵N chemical shifts	28	24	85.7

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	136	108	79.4
¹³C chemical shifts	136	96	70.6

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	90	47	52.2
¹³C chemical shifts	88	0	0.0
¹⁵N chemical shifts	2	2	100.0

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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 203, Sequence coverage: 97.5%
- Total number of restraints: 4816
- Weight of restraints: 1.0 (4816)
- Potential type of restraints: square-well-parabolic (4816)
- Range of distance target values: 1.53, 4.22 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 203, Sequence coverage: 88.7%
- Total number of restraints: 351
- Total number of restraints per polymer type: 351
- Weight of restraints: 1.0 (351)
- Potential type of restraints: square-well-parabolic (351)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords cytolysin fold, modified Greek key topology