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Found 1 Document (0.689 seconds)

BMRB: 19452

6AMR

Solution NMR structure of a putative thioredoxin (ECH_0218) in the reduced state from Ehrlichia chaffeensis, the etiological agent responsible for human monocytic ehrlichiosis. Seattle Structural Genomics Center for Infectious Disease target EhchA.00546.a

Authors

Buchko, G.W.

Assembly

putative thioredoxin (ECH 0218) in the reduced state from Ehrlichia chaffeensis

Entity

1. putative thioredoxin (ECH 0218) in the reduced state from Ehrlichia chaffeensis (polymer, Thiol state: all free), 120 monomers, 13321.97 Da Detail

MGTLEAQTQG PGSMIEQIGD SEFDNKVTSC NDNILILVDF WAPWCGPCRS LEPQLEKLAQ QYTENVKIYK INIEDNQDVA TQYGVSAIPT ILMFKNGKKL SQVIGADISK IISEINNNIN

Formula weight

13321.97 Da

Source organism

Ehrlichia chaffeensis str. Arkansas

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.3 %, Completeness: 76.1 %, Completeness (bb): 83.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.1 % (1067 of 1403)	72.4 % (529 of 731)	79.1 % (423 of 535)	83.9 % (115 of 137)
Backbone	83.1 % (590 of 710)	80.2 % (195 of 243)	83.8 % (295 of 352)	87.0 % (100 of 115)
Sidechain	71.2 % (573 of 805)	68.4 % (334 of 488)	75.9 % (224 of 295)	68.2 % (15 of 22)
Aromatic	53.8 % (42 of 78)	53.8 % (21 of 39)	56.8 % (21 of 37)	0.0 % (0 of 2)
Methyl	79.3 % (111 of 140)	77.1 % (54 of 70)	81.4 % (57 of 70)

1. entity

MGTLEAQTQG PGSMIEQIGD SEFDNKVTSC NDNILILVDF WAPWCGPCRS LEPQLEKLAQ QYTENVKIYK INIEDNQDVA TQYGVSAIPT ILMFKNGKKL SQVIGADISK IISEINNNIN

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 (±2.0) mM
2	TRIS	natural abundance	20 (±0.5) mM
3	DTT	natural abundance	1 (±0.2) mM
4	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
7	sodium chloride	natural abundance	100 (±2.0) mM
8	TRIS	natural abundance	20 (±0.5) mM
9	DTT	natural abundance	1 (±0.2) mM
10	entity	[U-99% 15N]	1 (±0.2) mM
11	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: 0.16 ppm, Outliers: 3 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: 0.16 ppm, Outliers: 3 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: -0.13 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: 0.07 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2016-05-25

Citation

Solution structure of the Ehrlichia chaffeensis thioredoxin ECH_0218 in the reduced state: disorder around the CXXC active site
Buchko, G.W., Hewitt, S.N., Van Voorhis, W.C., Myler, P.J.
Not known

Related entities 1. putative thioredoxin (ECH 0218) in the reduced state from Ehrlichia chaffeensis, : 1 : 1 : 84 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 (±2.0) mM
2	TRIS	natural abundance	20 (±0.5) mM
3	DTT	natural abundance	1 (±0.2) mM
4	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

2 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 (±2.0) mM
2	TRIS	natural abundance	20 (±0.5) mM
3	DTT	natural abundance	1 (±0.2) mM
4	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

3 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 (±2.0) mM
2	TRIS	natural abundance	20 (±0.5) mM
3	DTT	natural abundance	1 (±0.2) mM
4	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

4 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 (±2.0) mM
2	TRIS	natural abundance	20 (±0.5) mM
3	DTT	natural abundance	1 (±0.2) mM
4	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 (±2.0) mM
2	TRIS	natural abundance	20 (±0.5) mM
3	DTT	natural abundance	1 (±0.2) mM
4	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

6 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 (±2.0) mM
2	TRIS	natural abundance	20 (±0.5) mM
3	DTT	natural abundance	1 (±0.2) mM
4	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

7 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 (±2.0) mM
2	TRIS	natural abundance	20 (±0.5) mM
3	DTT	natural abundance	1 (±0.2) mM
4	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 (±2.0) mM
2	TRIS	natural abundance	20 (±0.5) mM
3	DTT	natural abundance	1 (±0.2) mM
4	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

9 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 (±2.0) mM
2	TRIS	natural abundance	20 (±0.5) mM
3	DTT	natural abundance	1 (±0.2) mM
4	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

10 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 (±2.0) mM
2	TRIS	natural abundance	20 (±0.5) mM
3	DTT	natural abundance	1 (±0.2) mM
4	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

11 deuterium exchange

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
7	sodium chloride	natural abundance	100 (±2.0) mM
8	TRIS	natural abundance	20 (±0.5) mM
9	DTT	natural abundance	1 (±0.2) mM
10	entity	[U-99% 15N]	1 (±0.2) mM
11	D2O	natural abundance	100 %

12 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 (±2.0) mM
2	TRIS	natural abundance	20 (±0.5) mM
3	DTT	natural abundance	1 (±0.2) mM
4	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

13 2D HBCBCGCDCDHD

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 (±2.0) mM
2	TRIS	natural abundance	20 (±0.5) mM
3	DTT	natural abundance	1 (±0.2) mM
4	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

14 2D HBCBCGCDCEHE

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 (±2.0) mM
2	TRIS	natural abundance	20 (±0.5) mM
3	DTT	natural abundance	1 (±0.2) mM
4	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19452_6amr.nef
Input source #2: Coordindates	6amr.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
MAHHHHHHMGTLEAQTQGPGSMIEQIGDSEFDNKVTSCNDNILILVDFWAPWCGPCRSLEPQLEKLAQQYTENVKIYKINIEDNQDVATQYGVSAIPTIL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAHHHHHHMGTLEAQTQGPGSMIEQIGDSEFDNKVTSCNDNILILVDFWAPWCGPCRSLEPQLEKLAQQYTENVKIYKINIEDNQDVATQYGVSAIPTIL

-------110-------120--------
MFKNGKKLSQVIGADISKIISEINNNIN
||||||||||||||||||||||||||||
MFKNGKKLSQVIGADISKIISEINNNIN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	128	0	0	100.0

Content subtype: combined_19452_6amr.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1031		79.7 (chain: A, length: 128)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	1847 (1)	noe	71.1 (chain: A, length: 128)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	64 (1)	hbond	39.1 (chain: A, length: 128)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	150 (150)	.	70.3 (chain: A, length: 128)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 79.7%
- Total number of assignments
  - ¹³C chemical shifts: 410
  - ¹H chemical shifts: 512
  - ¹⁵N chemical shifts: 109
- 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)
32	ASP	CG	8.33

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	573	409	71.4
¹H chemical shifts	777	512	65.9
¹⁵N chemical shifts	146	109	74.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	256	190	74.2
¹H chemical shifts	259	187	72.2
¹⁵N chemical shifts	123	96	78.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	317	219	69.1
¹H chemical shifts	518	325	62.7
¹⁵N chemical shifts	23	13	56.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	75	57	76.0
¹H chemical shifts	75	52	69.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	49	21	42.9
¹H chemical shifts	51	21	41.2
¹⁵N chemical shifts	2	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 71.1%
- Total number of restraints: 1847
- Weight of restraints: 1.0 (1847)
- Potential type of restraints: square-well-parabolic (1847)
- Range of distance target values: 2.25, 3.92 (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
- Saveframe: CNS/XPLOR_distance_constraints_2
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 39.1%
  - Total number of restraints: 64
  - Weight of restraints: 1.0 (64)
  - Potential type of restraints: square-well-parabolic (64)
  - Range of distance target values: 1.0, 1.75 (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: 128, Sequence coverage: 70.3%
- Total number of restraints: 150
- Total number of restraints per polymer type: 150
- Weight of restraints: 1.0 (150)
- Potential type of restraints: square-well-parabolic (150)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords SSGCID, human monocytic ehrlichiosis, infectious diseases, thioredoxin, tick diseases

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Found 1 Document (0.689 seconds)

BMRB: 19452

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. putative thioredoxin (ECH 0218) in the reduced state from Ehrlichia chaffeensis, : 1 : 1 : 84 entities Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 5 contents Detail