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Found 1 Document (0.68 seconds)

BMRB: 16101

2KD0

NMR solution Structure of O64736 protein from Arabidopsis thaliana:Northeast Structural Genomics Consortium MEGA Target AR3445A

Authors

G. V. T, S., Shastry, R., Foote, E., Ciccosanti, C., Jiang, M., Xiao, R., Nair, R., Everett, J., Huang, Y., Acton, T., Rost, B., Montelione, G.T.

Assembly

AR3445A

Entity

1. AR3445A (polymer, Thiol state: all free), 85 monomers, 9178.642 Da Detail

MGHHHHHHSH STIKLTVKFG GKSIPLSVSP DCTVKDLKSQ LQPITNVLPR GQKLIFKGKV LVETSTLKQS DVGSGAKLML MASQG

Formula weight

9178.642 Da

Source organism

Arabidopsis thaliana

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.6 %, Completeness: 88.9 %, Completeness (bb): 88.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.9 % (876 of 985)	88.7 % (455 of 513)	89.4 % (344 of 385)	88.5 % (77 of 87)
Backbone	88.8 % (446 of 502)	88.5 % (154 of 174)	89.5 % (221 of 247)	87.7 % (71 of 81)
Sidechain	89.1 % (499 of 560)	88.8 % (301 of 339)	89.3 % (192 of 215)	100.0 % (6 of 6)
Aromatic	41.7 % (20 of 48)	41.7 % (10 of 24)	41.7 % (10 of 24)
Methyl	100.0 % (100 of 100)	100.0 % (50 of 50)	100.0 % (50 of 50)

1. AR3445A

MGHHHHHHSH STIKLTVKFG GKSIPLSVSP DCTVKDLKSQ LQPITNVLPR GQKLIFKGKV LVETSTLKQS DVGSGAKLML MASQG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 6.5, Details 1.8mM AR3445A protein in 200mM NaCl, 5mM CaCl2, DSS at pH 6.5

#	Name	Isotope labeling	Concentration
1	sample_1	[U-100% 13C; U-100% 15N]	1.8 (±0.1) mM
2	CaCL2	natural abundance	5.0 mM
3	NACL	natural abundance	200 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 6.5, Details 1.8mM protein, 200mM NaCl, 5mM CaCl2

#	Name	Isotope labeling	Concentration
4	sample_2	[U-10% 13C; U-100% 15N]	1.80 (±0.1) mM
5	CaCL2	natural abundance	5.0 mM
6	NACL	natural abundance	200 mM

LACS Plot; CA

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

Referencing offset: -0.3 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.3 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.11 ppm, Outliers: 3 Detail

LACS Plot; CO

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

Referencing offset: 0.1 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KD0, Strand ID: A Detail

Release date

2009-02-18

Citation

NMR solution structure of O64736 protein from Arabidopsis thaliana
G. V. T, S., Montelione, G.
Not known, DOI O64736

Related entities 1. AR3445A, : 47 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 6.5, Details 1.8mM AR3445A protein in 200mM NaCl, 5mM CaCl2, DSS at pH 6.5

#	Name	Isotope labeling	Concentration
1	sample_1	[U-100% 13C; U-100% 15N]	1.8 (±0.1) mM
2	CaCL2	natural abundance	5.0 mM
3	NACL	natural abundance	200 mM

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 6.5, Details 1.8mM protein, 200mM NaCl, 5mM CaCl2

#	Name	Isotope labeling	Concentration
4	sample_2	[U-10% 13C; U-100% 15N]	1.80 (±0.1) mM
5	CaCL2	natural abundance	5.0 mM
6	NACL	natural abundance	200 mM

3 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 6.5, Details 1.8mM protein, 200mM NaCl, 5mM CaCl2

#	Name	Isotope labeling	Concentration
4	sample_2	[U-10% 13C; U-100% 15N]	1.80 (±0.1) mM
5	CaCL2	natural abundance	5.0 mM
6	NACL	natural abundance	200 mM

4 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 6.5, Details 1.8mM AR3445A protein in 200mM NaCl, 5mM CaCl2, DSS at pH 6.5

#	Name	Isotope labeling	Concentration
1	sample_1	[U-100% 13C; U-100% 15N]	1.8 (±0.1) mM
2	CaCL2	natural abundance	5.0 mM
3	NACL	natural abundance	200 mM

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 6.5, Details 1.8mM AR3445A protein in 200mM NaCl, 5mM CaCl2, DSS at pH 6.5

#	Name	Isotope labeling	Concentration
1	sample_1	[U-100% 13C; U-100% 15N]	1.8 (±0.1) mM
2	CaCL2	natural abundance	5.0 mM
3	NACL	natural abundance	200 mM

6 3D HNCACB

Instrument

Bruker Avance - 800 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 6.5, Details 1.8mM AR3445A protein in 200mM NaCl, 5mM CaCl2, DSS at pH 6.5

#	Name	Isotope labeling	Concentration
1	sample_1	[U-100% 13C; U-100% 15N]	1.8 (±0.1) mM
2	CaCL2	natural abundance	5.0 mM
3	NACL	natural abundance	200 mM

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 6.5, Details 1.8mM AR3445A protein in 200mM NaCl, 5mM CaCl2, DSS at pH 6.5

#	Name	Isotope labeling	Concentration
1	sample_1	[U-100% 13C; U-100% 15N]	1.8 (±0.1) mM
2	CaCL2	natural abundance	5.0 mM
3	NACL	natural abundance	200 mM

8 3D HNCO

Instrument

Bruker Avance - 800 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 6.5, Details 1.8mM AR3445A protein in 200mM NaCl, 5mM CaCl2, DSS at pH 6.5

#	Name	Isotope labeling	Concentration
1	sample_1	[U-100% 13C; U-100% 15N]	1.8 (±0.1) mM
2	CaCL2	natural abundance	5.0 mM
3	NACL	natural abundance	200 mM

9 3D HBHANH

Instrument

Bruker Avance - 600 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 6.5, Details 1.8mM AR3445A protein in 200mM NaCl, 5mM CaCl2, DSS at pH 6.5

#	Name	Isotope labeling	Concentration
1	sample_1	[U-100% 13C; U-100% 15N]	1.8 (±0.1) mM
2	CaCL2	natural abundance	5.0 mM
3	NACL	natural abundance	200 mM

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 6.5, Details 1.8mM AR3445A protein in 200mM NaCl, 5mM CaCl2, DSS at pH 6.5

#	Name	Isotope labeling	Concentration
1	sample_1	[U-100% 13C; U-100% 15N]	1.8 (±0.1) mM
2	CaCL2	natural abundance	5.0 mM
3	NACL	natural abundance	200 mM

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 6.5, Details 1.8mM AR3445A protein in 200mM NaCl, 5mM CaCl2, DSS at pH 6.5

#	Name	Isotope labeling	Concentration
1	sample_1	[U-100% 13C; U-100% 15N]	1.8 (±0.1) mM
2	CaCL2	natural abundance	5.0 mM
3	NACL	natural abundance	200 mM

12 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz Equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 6.5, Details 1.8mM AR3445A protein in 200mM NaCl, 5mM CaCl2, DSS at pH 6.5

#	Name	Isotope labeling	Concentration
1	sample_1	[U-100% 13C; U-100% 15N]	1.8 (±0.1) mM
2	CaCL2	natural abundance	5.0 mM
3	NACL	natural abundance	200 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16101_2kd0.nef
Input source #2: Coordindates	2kd0.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-----
MGHHHHHHSHSTIKLTVKFGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLMLMASQG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHSHSTIKLTVKFGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLMLMASQG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	85	0	0	100.0

Content subtype: combined_16101_2kd0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	876		89.4 (chain: A, length: 85)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1702 (1)	noe	88.2 (chain: A, length: 85)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	85 (85)	.	75.3 (chain: A, length: 85)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 89.4%
- Total number of assignments
  - ¹H chemical shifts: 458
  - ¹³C chemical shifts: 342
  - ¹⁵N chemical shifts: 76
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
66	THR	HG1	6.08

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	513	457	89.1
¹³C chemical shifts	385	342	88.8
¹⁵N chemical shifts	88	76	86.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	174	154	88.5
¹³C chemical shifts	170	152	89.4
¹⁵N chemical shifts	81	70	86.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	339	303	89.4
¹³C chemical shifts	215	190	88.4
¹⁵N chemical shifts	7	6	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	51	96.2
¹³C chemical shifts	53	51	96.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	10	41.7
¹³C chemical shifts	24	10	41.7

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 88.2%
- Total number of restraints: 1702
- Weight of restraints: 1.0 (1702)
- Potential type of restraints: square-well-parabolic (1702)
- Range of distance target values: 2.44, 4.44 (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: 85, Sequence coverage: 75.3%
- Total number of restraints: 85
- Total number of restraints per polymer type: 85
- Weight of restraints: 1.0 (85)
- Potential type of restraints: square-well-parabolic (85)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (0.68 seconds)

BMRB: 16101

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. AR3445A, : 47 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 4 contents Detail