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BMRB: 18607

2LW6

Solution structure of an avirulence protein AvrPzi-t from pathogen Magnaportheoryzae

Authors

Zhang, Z., Zhang, X., Zhou, Z., Hu, H., Liu, M., Zhou, B., Zhou, J.

Assembly

Avrpiz-t

Entity

1. Avrpiz-t (polymer, Thiol state: free and disulfide bound), 80 monomers, 8736.874 Da Detail

SFVQCNHHLL YNGRHWGTIR KKAGWAVRFY EEKPGQPKRL VAICKNASPV HCNYLKCTNL AAGFSAGTST DVLSSGTVGS

Formula weight

8736.874 Da

Source organism

Pyricularia oryzae

Exptl. method

solution NMR

Refine. method

distance geometry, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 89.2 %, Completeness (bb): 96.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.2 % (811 of 909)	89.8 % (421 of 469)	86.4 % (306 of 354)	97.7 % (84 of 86)
Backbone	96.2 % (456 of 474)	93.9 % (155 of 165)	97.8 % (227 of 232)	96.1 % (74 of 77)
Sidechain	82.2 % (417 of 507)	85.9 % (261 of 304)	75.8 % (147 of 194)	100.0 % (9 of 9)
Aromatic	38.3 % (36 of 94)	66.0 % (31 of 47)	6.7 % (3 of 45)	100.0 % (2 of 2)
Methyl	92.5 % (74 of 80)	92.5 % (37 of 40)	92.5 % (37 of 40)

1. Avrpiz-t

SFVQCNHHLL YNGRHWGTIR KKAGWAVRFY EEKPGQPKRL VAICKNASPV HCNYLKCTNL AAGFSAGTST DVLSSGTVGS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Avrpiz-t	[U-100% 13C; U-100% 15N]	0.3 mM
2	D2O	natural abundance	90 %
3	H2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
4	Avrpiz-t	[U-100% 15N]		0.3 mM
5	D2O	natural abundance		100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 1.11 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LW6, Strand ID: A Detail

Release date

2013-02-13

Citation

Solution structure of the Magnaporthe oryzae avirulence protein AvrPiz-t
Zhang, Z., Zhang, X., Zhou, Z., Hu, H., Liu, M., Zhou, B., Zhou, J.
J. Biomol. NMR (2013), 55, 219-223, PubMed 23334361 , DOI 10.1007/s10858-012-9695-5 , Abstract

Related entities 1. Avrpiz-t, : 1 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Avrpiz-t	[U-100% 13C; U-100% 15N]	0.3 mM
2	D2O	natural abundance	90 %
3	H2O	natural abundance	10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Avrpiz-t	[U-100% 13C; U-100% 15N]	0.3 mM
2	D2O	natural abundance	90 %
3	H2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Avrpiz-t	[U-100% 13C; U-100% 15N]	0.3 mM
2	D2O	natural abundance	90 %
3	H2O	natural abundance	10 %

4 3D HNCO

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Avrpiz-t	[U-100% 13C; U-100% 15N]	0.3 mM
2	D2O	natural abundance	90 %
3	H2O	natural abundance	10 %

5 3D HNCA

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Avrpiz-t	[U-100% 13C; U-100% 15N]	0.3 mM
2	D2O	natural abundance	90 %
3	H2O	natural abundance	10 %

6 3D HN(CO)CA

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Avrpiz-t	[U-100% 13C; U-100% 15N]	0.3 mM
2	D2O	natural abundance	90 %
3	H2O	natural abundance	10 %

7 3D HCCH-TOCSY

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Avrpiz-t	[U-100% 13C; U-100% 15N]	0.3 mM
2	D2O	natural abundance	90 %
3	H2O	natural abundance	10 %

8 3D 1H-15N TOCSY

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Avrpiz-t	[U-100% 13C; U-100% 15N]	0.3 mM
2	D2O	natural abundance	90 %
3	H2O	natural abundance	10 %

9 2D 1H-15N HSQC

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
4	Avrpiz-t	[U-100% 15N]		0.3 mM
5	D2O	natural abundance		100 %

10 3D 1H-13C NOESY

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Avrpiz-t	[U-100% 13C; U-100% 15N]	0.3 mM
2	D2O	natural abundance	90 %
3	H2O	natural abundance	10 %

11 3D HNCACB

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Avrpiz-t	[U-100% 13C; U-100% 15N]	0.3 mM
2	D2O	natural abundance	90 %
3	H2O	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_18607_2lw6.nef
Input source #2: Coordindates	2lw6.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:62:CYS:SG	A:75:CYS:SG	oxidized, CA 54.942, CB 51.384 ppm	oxidized, CA 55.634, CB 48.554 ppm	2.032

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

-20-------30--------40--------50--------60--------70--------80--------90--------
SFVQCNHHLLYNGRHWGTIRKKAGWAVRFYEEKPGQPKRLVAICKNASPVHCNYLKCTNLAAGFSAGTSTDVLSSGTVGS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SFVQCNHHLLYNGRHWGTIRKKAGWAVRFYEEKPGQPKRLVAICKNASPVHCNYLKCTNLAAGFSAGTSTDVLSSGTVGS
--------10--------20--------30--------40--------50--------60--------70--------80

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	80	0	0	100.0

Content subtype: combined_18607_2lw6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	806		98.8 (chain: A, length: 80)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	44 (1)	hbond	27.5 (chain: A, length: 80)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	61 (61)	.	58.8 (chain: A, length: 80)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 98.8%
- Total number of assignments
  - ¹H chemical shifts: 419
  - ¹³C chemical shifts: 302
  - ¹⁵N chemical shifts: 85
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
25	HIS	HD1	10.757
25	HIS	ND1	126.775
26	HIS	HD1	7.324
33	HIS	HD1	6.837
69	HIS	HD1	7.111

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	469	415	88.5
¹³C chemical shifts	354	302	85.3
¹⁵N chemical shifts	90	84	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	165	154	93.3
¹³C chemical shifts	160	154	96.3
¹⁵N chemical shifts	77	75	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	304	261	85.9
¹³C chemical shifts	194	148	76.3
¹⁵N chemical shifts	13	9	69.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	40	39	97.5
¹³C chemical shifts	40	39	97.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	28	59.6
¹³C chemical shifts	45	0	0.0
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: hbond
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 27.5%
- Total number of restraints: 44
- Weight of restraints: 1.0 (44)
- Potential type of restraints: square-well-parabolic (44)
- Range of distance target values: 1.9, 2.9 (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: 80, Sequence coverage: 58.8%
- Total number of restraints: 61
- Total number of restraints per polymer type: 61
- Weight of restraints: 1.0 (61)
- Potential type of restraints: square-well-parabolic (61)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords avirulence protein, AvrPiz-t, plant resistance gene, protein degradation

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Found 1 Document (0.48 seconds)

BMRB: 18607

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Avrpiz-t, : 1 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 4 contents Detail