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Found 1 Document (0.603 seconds)

BMRB: 18812

2M0N

Solution structure of a DUF3349 annotated protein from Mycobacterium abscessus, MAB_3403c. Seattle Structural Genomics Center for Infectious Disease target Myab.17112.a

Authors

Buchko, G.W.

Assembly

DUF3349

Entity

1. DUF3349 (polymer, Thiol state: not present), 112 monomers, 11996.22 Da Detail

MAHHHHHHMG TLEAQTQGPG SPEGVPPTDR FPLLALLRRT LTEEQVQEVV AKLTDPESSA QIDGVVSKDE IEKFIADVTK DEPTAQDISR VASRLAAGGW PLAGVDSTAL NA

Formula weight

11996.22 Da

Source organism

Mycobacteroides abscessus

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.9 %, Completeness: 80.4 %, Completeness (bb): 86.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.4 % (982 of 1222)	78.5 % (494 of 629)	81.1 % (390 of 481)	87.5 % (98 of 112)
Backbone	86.4 % (567 of 656)	87.1 % (195 of 224)	85.1 % (279 of 328)	89.4 % (93 of 104)
Sidechain	75.8 % (508 of 670)	73.8 % (299 of 405)	79.4 % (204 of 257)	62.5 % (5 of 8)
Aromatic	42.9 % (24 of 56)	42.9 % (12 of 28)	40.7 % (11 of 27)	100.0 % (1 of 1)
Methyl	86.8 % (118 of 136)	89.7 % (61 of 68)	83.8 % (57 of 68)

1. entity

MAHHHHHHMG TLEAQTQGPG SPEGVPPTDR FPLLALLRRT LTEEQVQEVV AKLTDPESSA QIDGVVSKDE IEKFIADVTK DEPTAQDISR VASRLAAGGW PLAGVDSTAL NA

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.1) mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
6	sodium chloride	natural abundance	100 (±2.0) mM
7	TRIS	natural abundance	20 (±1.0) mM
8	DTT	natural abundance	1 (±0.1) mM

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: 0.0 ppm, Outliers: 1 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: 0.0 ppm, Outliers: 1 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: 0.0 ppm, Outliers: 2 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: -0.3 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M0N, Strand ID: A Detail

Release date

2012-11-29

Citation

Evidence for further structural diversity in the DUF3349 family
Buchko, G.W., Hewitt, S.N., Van Voorhis, W.C., Myler, P.J.
Not known

Related entities 1. DUF3349, : 1 : 6 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 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.1) mM

2 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.1) mM

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.1) mM

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.1) mM

5 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.1) mM

6 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.1) mM

7 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.1) mM

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.1) mM

9 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.1) mM

10 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.1) mM

11 2D HBCBCGCDCDHD

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.1) mM

12 2D HBCBCGCDCEHE

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.1) mM

13 deuterium exchange

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
6	sodium chloride	natural abundance	100 (±2.0) mM
7	TRIS	natural abundance	20 (±1.0) mM
8	DTT	natural abundance	1 (±0.1) mM

14 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1.0 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±1.0) mM
4	DTT	natural abundance	1 (±0.1) mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18812_2m0n.nef
Input source #2: Coordindates	2m0n.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
MAHHHHHHMGTLEAQTQGPGSPEGVPPTDRFPLLALLRRTLTEEQVQEVVAKLTDPESSAQIDGVVSKDEIEKFIADVTKDEPTAQDISRVASRLAAGGW
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAHHHHHHMGTLEAQTQGPGSPEGVPPTDRFPLLALLRRTLTEEQVQEVVAKLTDPESSAQIDGVVSKDEIEKFIADVTKDEPTAQDISRVASRLAAGGW

-------110--
PLAGVDSTALNA
||||||||||||
PLAGVDSTALNA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	112	0	0	100.0

Content subtype: combined_18812_2m0n.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	943		91.1 (chain: A, length: 112)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1365 (1)	noe	83.0 (chain: A, length: 112)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	42 (1)	hbond	28.6 (chain: A, length: 112)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	124 (124)	.	67.9 (chain: A, length: 112)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 112, Sequence coverage: 91.1%
- Total number of assignments
  - ¹H chemical shifts: 471
  - ¹³C chemical shifts: 376
  - ¹⁵N chemical shifts: 96
- 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	629	471	74.9
¹³C chemical shifts	481	376	78.2
¹⁵N chemical shifts	117	96	82.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	224	191	85.3
¹³C chemical shifts	224	180	80.4
¹⁵N chemical shifts	104	91	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	405	280	69.1
¹³C chemical shifts	257	196	76.3
¹⁵N chemical shifts	13	5	38.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	61	87.1
¹³C chemical shifts	70	56	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	12	42.9
¹³C chemical shifts	27	11	40.7
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 112, Sequence coverage: 83.0%
- Total number of restraints: 1365
- Weight of restraints: 1.0 (1365)
- Potential type of restraints: square-well-parabolic (1365)
- Range of distance target values: 2.19, 3.71 (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_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 112, Sequence coverage: 28.6%
  - Total number of restraints: 42
  - Weight of restraints: 1.0 (42)
  - Potential type of restraints: square-well-parabolic (42)
  - Range of distance target values: 1.9, 2.85 (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: 112, Sequence coverage: 67.9%
- Total number of restraints: 124
- Total number of restraints per polymer type: 124
- Weight of restraints: 1.0 (124)
- Potential type of restraints: square-well-parabolic (124)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords infectious diseases, NMR spectroscopy, SSGCID, tuberculosis

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Found 1 Document (0.603 seconds)

BMRB: 18812

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. DUF3349, : 1 : 6 entities Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 5 contents Detail