BMRBj - BMREntryMaster

Found 1 Document (0.51 seconds)

BMRB: 25944

2NAR

Solution structure of AVR3a_60-147 from Phytophthora infestans

Authors

Matena, A., Bayer, P., Zhukov, I., Stanek, J., Kozminski, W., van West, P., Wawra, S.

Assembly

AVR3a 60-147 from Phytophthora infestans

Entity

1. AVR3a 60-147 from Phytophthora infestans (polymer, Thiol state: not present), 102 monomers, 11496.96 Da Detail

PNFNLASLNE EMFNVAALTK RADAKKLAKQ LMGNDKLADA AYIWWQHNRV TLDQIDTFLK LASRKTQGAK YNQIYNSYMM HLGLTGYEPN SSSVDKLAAA LE

Formula weight

11496.96 Da

Source organism

Phytophthora infestans

Exptl. method

Refine. method

simulated annealing, energy minimization

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.1 %, Completeness: 84.1 %, Completeness (bb): 94.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.1 % (1013 of 1205)	86.2 % (539 of 625)	80.2 % (372 of 464)	87.9 % (102 of 116)
Backbone	94.9 % (577 of 608)	93.7 % (193 of 206)	95.4 % (288 of 302)	96.0 % (96 of 100)
Sidechain	76.0 % (528 of 695)	82.6 % (346 of 419)	67.7 % (176 of 260)	37.5 % (6 of 16)
Aromatic	53.9 % (55 of 102)	88.2 % (45 of 51)	16.3 % (8 of 49)	100.0 % (2 of 2)
Methyl	93.0 % (106 of 114)	93.0 % (53 of 57)	93.0 % (53 of 57)

1. entity

PNFNLASLNE EMFNVAALTK RADAKKLAKQ LMGNDKLADA AYIWWQHNRV TLDQIDTFLK LASRKTQGAK YNQIYNSYMM HLGLTGYEPN SSSVDKLAAA LE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	Potassium phosphate	natural abundance		50 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		90 %
9	DSS	natural abundance		50 uM
10	entity	[U-100% 15N]		300 uM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
11	Potassium phosphate	natural abundance		50 mM
12	D2O	natural abundance		10 %
13	H2O	natural abundance		90 %
14	DSS	natural abundance		50 uM
15	entity	[U-100% 13C; U-100% 15N]		300 uM

LACS Plot; CA

Referencing offset: -0.14 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.14 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.37 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2NAR, Strand ID: A Detail

Release date

2016-01-13

Citation

The RxLR Motif of the Host Targeting Effector AVR3a of Phytophthora infestans Is Cleaved before Secretion
Wawra, S., Trusch, F., Matena, A., Apostolakis, K., Linne, U., Zhukov, I., Stanek, J., Kozminski, W., Davidson, I., Secombes, C.J., Bayer, P., van West, P.
Plant Cell (2017), 29, 1184-1195, PubMed 28522546 , DOI 10.1105/tpc.16.00552 , Abstract

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

2 2D 1H-1H COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

5 3D HCCH-COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

7 3D HBHANH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

9 13C-NOESY-HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

10 15N-NOESY-HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

11 3D HNCO

Instrument

Varian VNMRS - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

12 4D HNCOCA

Instrument

Varian VNMRS - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

13 4D HNCACO

Instrument

Varian VNMRS - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

14 4D HBHACBCANH

Instrument

Varian VNMRS - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Potassium phosphate	natural abundance		50 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	DSS	natural abundance		50 uM
5	entity	natural abundance		300 uM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25944_2nar.nef
Input source #2: Coordindates	2nar.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
PNFNLASLNEEMFNVAALTKRADAKKLAKQLMGNDKLADAAYIWWQHNRVTLDQIDTFLKLASRKTQGAKYNQIYNSYMMHLGLTGYEPNSSSVDKLAAA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PNFNLASLNEEMFNVAALTKRADAKKLAKQLMGNDKLADAAYIWWQHNRVTLDQIDTFLKLASRKTQGAKYNQIYNSYMMHLGLTGYEPNSSSVDKLAAA

--
LE
||
LE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	102	0	0	100.0

Content subtype: combined_25944_2nar.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	967		92.2 (chain: A, length: 102)
1	Distance restraints	DYANA/DIANA_distance_constraints_7	Warning	28 (1)	noe	2.9 (chain: A, length: 102)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	122 (122)	.	70.6 (chain: A, length: 102)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 92.2%
- Total number of assignments
  - ¹H chemical shifts: 514
  - ¹³C chemical shifts: 356
  - ¹⁵N chemical shifts: 97
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: DYANA/DIANA_distance_constraints_7
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 2.9%
- Total number of restraints: 28
- Weight of restraints: 1.0 (28)
- Potential type of restraints: upper-bound-parabolic (28)
- Range of distance target values: 3.3, 5.98 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 70.6%
- Total number of restraints: 122
- Total number of restraints per polymer type: 122
- Weight of restraints: 1.0 (122)
- Potential type of restraints: square-well-parabolic (122)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords all alpha