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Found 1 Document (0.779 seconds)

BMRB: 15584

2JY9

NMR STRUCTURE OF PUTATIVE-tRNA HYDROLASE DOMAIN FROM SALMONELLA TYPHIMURIUM: NORTH EAST STRUCTURAL GENOMICS CONSORTIUM TARGET STR220

Authors

SINGARAPU, K., WU, Y., SUKUMARAN, D., ELETSKY, A., ZERI, A., WANG, D., JANJUA, H., OWENS, L., XIAO, R., LIU, J., BARAN, M.C., G.V.T, S., ACTON, T.B., ROST, B., MONTELIONE, G.T., SZYPERSKI, T.

Assembly

STR220

Entity

1. STR220 (polymer, Thiol state: all free), 148 monomers, 16659.84 Da Detail

MIAISRTVSI ADNELEITAI RAQGAGGQHV NKTSSAIHLR FDIRASGLPE YYKQRLLTAS HHLISDDGVI IIKAQEFRSQ ELNREAAIAR LVAVIKELTA EQKSRRATRP TRASKERRLS SKAQKSSVKA LRGKVRRPLD LEHHHHHH

Formula weight

16659.84 Da

Source organism

Salmonella enterica subsp. enterica serovar Typhimurium

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.3 %, Completeness: 88.5 %, Completeness (bb): 91.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.5 % (1523 of 1721)	87.9 % (793 of 902)	88.7 % (589 of 664)	91.0 % (141 of 155)
Backbone	91.4 % (806 of 882)	92.0 % (275 of 299)	90.9 % (398 of 438)	91.7 % (133 of 145)
Sidechain	86.3 % (847 of 981)	85.9 % (518 of 603)	87.2 % (321 of 368)	80.0 % (8 of 10)
Aromatic	53.9 % (41 of 76)	63.2 % (24 of 38)	44.7 % (17 of 38)
Methyl	100.0 % (182 of 182)	100.0 % (91 of 91)	100.0 % (91 of 91)

1. STR220

MIAISRTVSI ADNELEITAI RAQGAGGQHV NKTSSAIHLR FDIRASGLPE YYKQRLLTAS HHLISDDGVI IIKAQEFRSQ ELNREAAIAR LVAVIKELTA EQKSRRATRP TRASKERRLS SKAQKSSVKA LRGKVRRPLD LEHHHHHH

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.4 mM
2	D2O	[U-100% 2H]	5 %
3	H2O		95 %

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: 0.06 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: 0.06 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: 0.0 ppm, Outliers: 4 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: 0.13 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JY9, Strand ID: A Detail

Release date

2008-01-17

Citation

NMR STRUCTURE OF PUTATIVE-tRNA HYDROLASE DOMAIN FROM SALMONELLA TYPHIMURIUM: NORTH EAST STRUCTURAL GENOMICS CONSORTIUM TARGET STR220
SINGARAPU, K., WU, Y., SUKUMARAN, D., ELETSKY, A., ZERI, A., WANG, D., JANJUA, H., OWENS, L., XIAO, R., LIU, J., BARAN, M.C., G.V.T, S., ACTON, T.B., ROST, B., MONTELIONE, G.T., SZYPERSKI, T.

Related entities 1. STR220, : 1 : 31 entities Detail

Experiments performed 8 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15584_2jy9.nef
Input source #2: Coordindates	2jy9.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
MIAISRTVSIADNELEITAIRAQGAGGQHVNKTSSAIHLRFDIRASGLPEYYKQRLLTASHHLISDDGVIIIKAQEFRSQELNREAAIARLVAVIKELTA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MIAISRTVSIADNELEITAIRAQGAGGQHVNKTSSAIHLRFDIRASGLPEYYKQRLLTASHHLISDDGVIIIKAQEFRSQELNREAAIARLVAVIKELTA

-------110-------120-------130-------140--------
EQKSRRATRPTRASKERRLSSKAQKSSVKALRGKVRRPLDLEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||
EQKSRRATRPTRASKERRLSSKAQKSSVKALRGKVRRPLDLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	148	0	0	100.0

Content subtype: combined_15584_2jy9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1518		95.9 (chain: A, length: 148)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1753 (1)	noe	87.2 (chain: A, length: 148)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	423 (415)	.	71.6 (chain: A, length: 148)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 95.9%
- Total number of assignments
  - ¹H chemical shifts: 793
  - ¹³C chemical shifts: 586
  - ¹⁵N chemical shifts: 139
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- 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	902	793	87.9
¹³C chemical shifts	664	586	88.3
¹⁵N chemical shifts	172	139	80.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	299	276	92.3
¹³C chemical shifts	296	268	90.5
¹⁵N chemical shifts	145	132	91.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	603	517	85.7
¹³C chemical shifts	368	318	86.4
¹⁵N chemical shifts	27	7	25.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	92	92	100.0
¹³C chemical shifts	92	92	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	23	60.5
¹³C chemical shifts	38	15	39.5

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 87.2%
- Total number of restraints: 1753
- Weight of restraints: 1.0 (1753)
- Potential type of restraints: upper-bound-parabolic (1753)
- Range of distance target values: 2.44, 10.7 (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: DYANA/DIANA_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 71.6%
- Total number of restraints: 415
- Total number of restraints per polymer type: 415
- Weight of restraints: 1.0 (415)
- Potential type of restraints: square-well-parabolic (415)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (0.779 seconds)

BMRB: 15584

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. STR220, : 1 : 31 entities Detail

Experiments performed 8 experiments Detail

Instrument

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NMR combined restraints 4 contents Detail