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Found 1 Document (0.728 seconds)

BMRB: 15585

2JYA

Solution structure of protein ATU1810 from Agrobacterium tumefaciens; Northeast Structural Genomics Target AtR23; Ontario Center for Structural Proteomics Target ATC1776

Authors

Lemak, A., Yee, A., Gutmanas, A., Fares, C., Karra, M., Semesi, A., Arrowsmith, C.H.

Assembly

ATU1810

Entity

1. ATU1810 (polymer, Thiol state: not present), 106 monomers, 12202.68 Da Detail

QGHMSAKIYR PAKTAMQSGT AKTNVWVLEF DAEVPRKIDP IMGYTSSSDM KQQVKLTFET QEQAEAYAQR KGIEYRVILP KEATRKVVSY TDNFRFNRTQ PWTHGS

Formula weight

12202.68 Da

Source organism

Agrobacterium tumefaciens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.2 %, Completeness: 89.1 %, Completeness (bb): 92.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.1 % (1130 of 1268)	90.1 % (599 of 665)	87.5 % (428 of 489)	90.4 % (103 of 114)
Backbone	92.5 % (579 of 626)	92.9 % (197 of 212)	92.3 % (289 of 313)	92.1 % (93 of 101)
Sidechain	84.9 % (631 of 743)	87.0 % (394 of 453)	82.3 % (228 of 277)	69.2 % (9 of 13)
Aromatic	60.7 % (68 of 112)	73.2 % (41 of 56)	46.3 % (25 of 54)	100.0 % (2 of 2)
Methyl	93.9 % (92 of 98)	93.9 % (46 of 49)	93.9 % (46 of 49)

1. Atu1810

QGHMSAKIYR PAKTAMQSGT AKTNVWVLEF DAEVPRKIDP IMGYTSSSDM KQQVKLTFET QEQAEAYAQR KGIEYRVILP KEATRKVVSY TDNFRFNRTQ PWTHGS

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Concentration
1	Atu1810	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 %
5	benzamidine	natural abundance	10 mM
6	D2O	[U-100% 2H]	10 %
7	H2O		90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	Atu1810	[U-13C; U-15N]	0.5 mM
9	TRIS	natural abundance	10 mM
10	sodium chloride	natural abundance	300 mM
11	sodium azide	natural abundance	0.1 %
12	benzamidine	natural abundance	10 mM
13	D2O	[U-100% 2H]	100 %

LACS Plot; CA

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

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.08 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.25 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2009-04-22

Citation

Solution structure of protein ATU1810 form Agrobacterium tumefaciens
Lemak, A., Yee, A., Gutmanas, A., Fares, C., Karra, M., Semesi, A., Arrowsmith, C.H.

Related entities 1. ATU1810, : 1 : 45 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	Atu1810	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 %
5	benzamidine	natural abundance	10 mM
6	D2O	[U-100% 2H]	10 %
7	H2O		90 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	Atu1810	[U-13C; U-15N]	0.5 mM
9	TRIS	natural abundance	10 mM
10	sodium chloride	natural abundance	300 mM
11	sodium azide	natural abundance	0.1 %
12	benzamidine	natural abundance	10 mM
13	D2O	[U-100% 2H]	100 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	Atu1810	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 %
5	benzamidine	natural abundance	10 mM
6	D2O	[U-100% 2H]	10 %
7	H2O		90 %

4 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	Atu1810	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 %
5	benzamidine	natural abundance	10 mM
6	D2O	[U-100% 2H]	10 %
7	H2O		90 %

5 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	Atu1810	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 %
5	benzamidine	natural abundance	10 mM
6	D2O	[U-100% 2H]	10 %
7	H2O		90 %

6 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	Atu1810	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 %
5	benzamidine	natural abundance	10 mM
6	D2O	[U-100% 2H]	10 %
7	H2O		90 %

7 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	Atu1810	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 %
5	benzamidine	natural abundance	10 mM
6	D2O	[U-100% 2H]	10 %
7	H2O		90 %

8 3D (H)C(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	Atu1810	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 %
5	benzamidine	natural abundance	10 mM
6	D2O	[U-100% 2H]	10 %
7	H2O		90 %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	Atu1810	[U-13C; U-15N]	0.5 mM
9	TRIS	natural abundance	10 mM
10	sodium chloride	natural abundance	300 mM
11	sodium azide	natural abundance	0.1 %
12	benzamidine	natural abundance	10 mM
13	D2O	[U-100% 2H]	100 %

10 3D (H)CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	Atu1810	[U-13C; U-15N]	0.5 mM
9	TRIS	natural abundance	10 mM
10	sodium chloride	natural abundance	300 mM
11	sodium azide	natural abundance	0.1 %
12	benzamidine	natural abundance	10 mM
13	D2O	[U-100% 2H]	100 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	Atu1810	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 %
5	benzamidine	natural abundance	10 mM
6	D2O	[U-100% 2H]	10 %
7	H2O		90 %

12 3D 1H-13C NOESY_aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	Atu1810	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 %
5	benzamidine	natural abundance	10 mM
6	D2O	[U-100% 2H]	10 %
7	H2O		90 %

13 3D 1H-13C NOESY_aromatic

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	Atu1810	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 %
5	benzamidine	natural abundance	10 mM
6	D2O	[U-100% 2H]	10 %
7	H2O		90 %

14 2D 1H-15N HSQC(IPAP)

Instrument

Bruker Avance - 500 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	Atu1810	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 %
5	benzamidine	natural abundance	10 mM
6	D2O	[U-100% 2H]	10 %
7	H2O		90 %

15 3D TROSY-HNCO

Instrument

Bruker Avance - 500 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	Atu1810	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 %
5	benzamidine	natural abundance	10 mM
6	D2O	[U-100% 2H]	10 %
7	H2O		90 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_15585_2jya.nef
Input source #2: Coordindates	2jya.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-------
QGHMSAKIYRPAKTAMQSGTAKTNVWVLEFDAEVPRKIDPIMGYTSSSDMKQQVKLTFETQEQAEAYAQRKGIEYRVILPKEATRKVVSYTDNFRFNRTQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QGHMSAKIYRPAKTAMQSGTAKTNVWVLEFDAEVPRKIDPIMGYTSSSDMKQQVKLTFETQEQAEAYAQRKGIEYRVILPKEATRKVVSYTDNFRFNRTQ
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

100---
PWTHGS
||||||
PWTHGS
------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	106	0	0	100.0

Content subtype: combined_15585_2jya.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1099		95.3 (chain: A, length: 106)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2444 (1)	noe	93.4 (chain: A, length: 106)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	74 (74)	.	50.9 (chain: A, length: 106)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	72 (72)	.	37.7 (chain: A, length: 106)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 95.3%
- Total number of assignments
  - ¹H chemical shifts: 583
  - ¹³C chemical shifts: 416
  - ¹⁵N chemical shifts: 100
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	665	583	87.7
¹³C chemical shifts	489	416	85.1
¹⁵N chemical shifts	121	100	82.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	212	193	91.0
¹³C chemical shifts	212	190	89.6
¹⁵N chemical shifts	101	92	91.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	453	390	86.1
¹³C chemical shifts	277	226	81.6
¹⁵N chemical shifts	20	8	40.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	43	81.1
¹³C chemical shifts	53	43	81.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	41	73.2
¹³C chemical shifts	54	25	46.3
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 93.4%
- Total number of restraints: 2444
- Weight of restraints: 1.0 (2444)
- Potential type of restraints: square-well-parabolic (2444)
- Range of distance target values: 2.25, 3.9 (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: 106, Sequence coverage: 50.9%
- Total number of restraints: 74
- Total number of restraints per polymer type: 74
- Weight of restraints: 1.0 (74)
- Potential type of restraints: square-well-parabolic (74)
- 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: 106, Sequence coverage: 37.7%
- Total number of restraints: 72
- Potential type of restraints: undefined (72)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords protein with unknown function ATU1810

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Found 1 Document (0.728 seconds)

BMRB: 15585

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. ATU1810, : 1 : 45 entities Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 5 contents Detail