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BMRB: 17865

2LHT

Solution structure of Venturia inaequalis cellophane-induced 1 protein (ViCin1) domains 1 and 2

Authors

Mesarich, C.H., Schmitz, M., Tremouilhac, P., Greenwood, D.R., McGillivray, D.J., Templeton, M.D., Dingley, A.J.

Assembly

ViCin1-D1D2

Entity

1. ViCin1-D1D2 (polymer, Thiol state: all disulfide bound), 122 monomers, 13626.20 Da Detail

ADVFDPPTQY GYDGKPLDAS FCRTAGSREK DCRKDVQACD KKYDDQGRET ACAKGIREKY KPAVVYGYDG KPLDLGFCTL AGIREVDCRK DAQTCDKKYE SDKCLNAIKE KYKPVVDPNP PA

Formula weight

13626.2 Da

Source organism

Venturia inaequalis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, heteronucl_NOEs, heteronucl_T1_relaxation, heteronucl_T2_relaxation, spectral_density_values

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.7 %, Completeness (bb): 96.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.7 % (1318 of 1392)	95.5 % (703 of 736)	93.3 % (501 of 537)	95.8 % (114 of 119)
Backbone	96.6 % (690 of 714)	97.5 % (238 of 244)	96.4 % (344 of 357)	95.6 % (108 of 113)
Sidechain	93.7 % (741 of 791)	94.5 % (465 of 492)	92.2 % (270 of 293)	100.0 % (6 of 6)
Aromatic	68.1 % (64 of 94)	76.6 % (36 of 47)	59.6 % (28 of 47)
Methyl	96.7 % (89 of 92)	97.8 % (45 of 46)	95.7 % (44 of 46)

1. ViCin1-D1D2

ADVFDPPTQY GYDGKPLDAS FCRTAGSREK DCRKDVQACD KKYDDQGRET ACAKGIREKY KPAVVYGYDG KPLDLGFCTL AGIREVDCRK DAQTCDKKYE SDKCLNAIKE KYKPVVDPNP PA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
5	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	1.0 mM
6	potassium phosphate	natural abundance	25 mM
7	polyacrylamide gel	natural abundance	5-6 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

LACS Plot; CA

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

Referencing offset: 0.09 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.09 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.03 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: -0.21 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Heteronucl. T₁

94 T₁ values in 1 lists
Coherence Sz, Field strength (¹H) 600.17 MHz, Pressure 1 atm, Temperature 298.15 K, pH 6.2 Detail

Heteronucl. T₂

94 T₂ values in 1 lists
Coherence S(+,-), Field strength (¹H) 600.17 MHz, Pressure 1 atm, Temperature 298.15 K, pH 6.2 Detail

Heteronucl. NOE

94 NOE values in 1 lists
Value type peak height, Field strength (¹H) 600.17 MHz, Pressure 1 atm, Temperature 298.15 K, pH 6.2 Detail

Heteronucl. T₁/T₂

94 T₁/T₂ values in 1 lists
Field strength (¹H) 600.17 MHz, Pressure 1 atm, Temperature 298.15 K, pH 6.2 Detail

Spectral density

94 values in 1 lists
Pressure 1 atm, Temperature 298.15 K, pH 6.2 Detail

Release date

2012-07-15

Citation

Structure, dynamics and domain organization of the repeat protein Cin1 from the apple scab fungus
Mesarich, C.H., Schmitz, M., Tremouilhac, P., McGillivray, D.J., Templeton, M.D., Dingley, A.J.
Biochim. Biophys. Acta (2012), 1824, 1118-1128, PubMed 22771296 , DOI 10.1016/j.bbapap.2012.06.015 , Abstract

Related entities 1. ViCin1-D1D2, : 1 entities Detail

Experiments performed 21 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

2 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

3 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

4 3D CBCANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

6 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

7 3D HCAN

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

8 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

9 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

10 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

12 2D HBCBCGCDHG

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

13 2D HBCBCGCDCEHE

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

14 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

15 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

16 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

17 2D 1H-15N IPAP-HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

18 2D 1H-15N IPAP-HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
5	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	1.0 mM
6	potassium phosphate	natural abundance	25 mM
7	polyacrylamide gel	natural abundance	5-6 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

19 2D 1H-15N R2 relaxation

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

20 2D 1H-15N R1 relaxation

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

21 2D 1H-15N heteronuclear NOE

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	ViCin1-D1D2	[U-99% 13C; U-99% 15N]	0.6-0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17865_2lht.nef
Input source #2: Coordindates	2lht.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:47:CYS:SG	A:57:CYS:SG	oxidized, CA 53.6, CB 36.391 ppm	oxidized, CA 60.197, CB 33.966 ppm	2.027
A:64:CYS:SG	A:77:CYS:SG	oxidized, CA 51.88, CB 34.328 ppm	oxidized, CA 57.701, CB 35.631 ppm	2.032
A:103:CYS:SG	A:113:CYS:SG	oxidized 96.0%, reduced 4.0%, CA 53.696, CB 34.237 ppm	oxidized 44.8%, reduced 55.2%, CA 59.759, CB 33.835 ppm	2.031
A:120:CYS:SG	A:129:CYS:SG	oxidized, CA 52.973, CB 36.731 ppm	oxidized, CA 59.79, CB 36.879 ppm	2.029

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

---30--------40--------50--------60--------70--------80--------90-------100-------110-------120-----
ADVFDPPTQYGYDGKPLDASFCRTAGSREKDCRKDVQACDKKYDDQGRETACAKGIREKYKPAVVYGYDGKPLDLGFCTLAGIREVDCRKDAQTCDKKYE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ADVFDPPTQYGYDGKPLDASFCRTAGSREKDCRKDVQACDKKYDDQGRETACAKGIREKYKPAVVYGYDGKPLDLGFCTLAGIREVDCRKDAQTCDKKYE
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--130-------140-------
SDKCLNAIKEKYKPVVDPNPPA
||||||||||||||||||||||
SDKCLNAIKEKYKPVVDPNPPA
-------110-------120--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	122	0	0	100.0

Content subtype: combined_17865_2lht.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_chem_shift_list_1	Warning	1317		100.0 (chain: A, length: 122)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1769 (1)	noe	98.4 (chain: A, length: 122)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	186 (186)	.	91.0 (chain: A, length: 122)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	41 (41)	.	33.6 (chain: A, length: 122)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 122, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 704
  - ¹³C chemical shifts: 499
  - ¹⁵N chemical shifts: 114
- 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	736	703	95.5
¹³C chemical shifts	537	499	92.9
¹⁵N chemical shifts	126	114	90.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	244	238	97.5
¹³C chemical shifts	244	230	94.3
¹⁵N chemical shifts	113	108	95.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	492	465	94.5
¹³C chemical shifts	293	269	91.8
¹⁵N chemical shifts	13	6	46.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	45	97.8
¹³C chemical shifts	46	44	95.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	36	76.6
¹³C chemical shifts	47	28	59.6

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: 122, Sequence coverage: 98.4%
- Total number of restraints: 1763
- Weight of restraints: 1.0 (1763)
- Potential type of restraints: square-well-parabolic (1763)
- Range of distance target values: 2.4, 4.15 (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: 122, Sequence coverage: 91.0%
- Total number of restraints: 186
- Total number of restraints per polymer type: 186
- Weight of restraints: 1.0 (186)
- Potential type of restraints: square-well-parabolic (186)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 122, Sequence coverage: 33.6%
- Total number of restraints: 41
- Potential type of restraints: undefined (41)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords NMR structure, PROTEIN, secreted repeat domain, Venturia inaequalis

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Found 1 Document (0.714 seconds)

BMRB: 17865

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. ViCin1-D1D2, : 1 entities Detail

Experiments performed 21 experiments Detail

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NMR combined restraints 5 contents Detail