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Found 1 Document (0.736 seconds)

BMRB: 18487

2LTL

Solution NMR Structure of NifU-like protein from Saccharomyces cerevisiae, Northeast Structural Genomics Consortium (NESG) Target YR313A

Authors

Liu, G., Xiao, R., Hamilton, K., Janjua, H., Shastry, R., Kohan, E., Acton, T.B., Everett, J.K., Lee, H., Huang, Y.J., Montelione, G.T.

Assembly

YR313A

Entity

1. YR313A (polymer, Thiol state: all free), 119 monomers, 13617.42 Da Detail

MGHHHHHHSH MNSQRLIHIK TLTTPNENAL KFLSTDGEML QTRGSKSIVI KNTDENLINH SKLAQQIFLQ CPGVESLMIG DDFLTINKDR MVHWNSIKPE IIDLLTKQLA YGEDVISKE

Formula weight

13617.42 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

distance geometry, simulated annealing, torsion angle dynamics, molecular dynamics

Data set

RDCs, assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 92.4 %, Completeness: 84.1 %, Completeness (bb): 78.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.1 % (1191 of 1417)	90.4 % (667 of 738)	73.9 % (405 of 548)	90.8 % (119 of 131)
Backbone	78.2 % (554 of 708)	90.5 % (218 of 241)	66.1 % (232 of 351)	89.7 % (104 of 116)
Sidechain	90.1 % (741 of 822)	90.3 % (449 of 497)	89.4 % (277 of 310)	100.0 % (15 of 15)
Aromatic	58.9 % (53 of 90)	60.0 % (27 of 45)	56.8 % (25 of 44)	100.0 % (1 of 1)
Methyl	100.0 % (138 of 138)	100.0 % (69 of 69)	100.0 % (69 of 69)

1. YR313A

MGHHHHHHSH MNSQRLIHIK TLTTPNENAL KFLSTDGEML QTRGSKSIVI KNTDENLINH SKLAQQIFLQ CPGVESLMIG DDFLTINKDR MVHWNSIKPE IIDLLTKQLA YGEDVISKE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	YR313A.037	[U-100% 13C; U-100% 15N]	1.027 mM
2	NaCl	natural abundance	450 mM
3	Na2PO4	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	ZnSO4	natural abundance	20 uM
6	Proteinase inhibitors	natural abundance	1 na
7	NaN3	natural abundance	0.02 %
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.52 mM YR313A.037, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
10	YR313A.040	[U-10% 13C; U-100% 15N]	0.52 mM
11	NaCl	natural abundance	450 mM
12	Na2PO4	natural abundance	25 mM
13	DTT	natural abundance	10 mM
14	ZnSO4	natural abundance	20 uM
15	Proteinase inhibitors	natural abundance	1 na
16	NaN3	natural abundance	0.02 %
17	D2O	natural abundance	10 %
18	H2O	natural abundance	90 %

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: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.12 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

RDC

146 RDC values in 2 lists
Field strength (¹H) 599.520 MHz, Pressure 1 atm, Temperature 298 K, pH 6.5 Detail

Release date

2012-07-01

Related entities 1. YR313A, : 1 : 34 entities Detail

Interaction partners 1. YR313A, : 3 interactors Detail

More details for 3 interactors identified by 3 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	YR313A.037	[U-100% 13C; U-100% 15N]	1.027 mM
2	NaCl	natural abundance	450 mM
3	Na2PO4	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	ZnSO4	natural abundance	20 uM
6	Proteinase inhibitors	natural abundance	1 na
7	NaN3	natural abundance	0.02 %
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz at Rutgers

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.52 mM YR313A.037, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
10	YR313A.040	[U-10% 13C; U-100% 15N]	0.52 mM
11	NaCl	natural abundance	450 mM
12	Na2PO4	natural abundance	25 mM
13	DTT	natural abundance	10 mM
14	ZnSO4	natural abundance	20 uM
15	Proteinase inhibitors	natural abundance	1 na
16	NaN3	natural abundance	0.02 %
17	D2O	natural abundance	10 %
18	H2O	natural abundance	90 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	YR313A.037	[U-100% 13C; U-100% 15N]	1.027 mM
2	NaCl	natural abundance	450 mM
3	Na2PO4	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	ZnSO4	natural abundance	20 uM
6	Proteinase inhibitors	natural abundance	1 na
7	NaN3	natural abundance	0.02 %
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	YR313A.037	[U-100% 13C; U-100% 15N]	1.027 mM
2	NaCl	natural abundance	450 mM
3	Na2PO4	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	ZnSO4	natural abundance	20 uM
6	Proteinase inhibitors	natural abundance	1 na
7	NaN3	natural abundance	0.02 %
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	YR313A.037	[U-100% 13C; U-100% 15N]	1.027 mM
2	NaCl	natural abundance	450 mM
3	Na2PO4	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	ZnSO4	natural abundance	20 uM
6	Proteinase inhibitors	natural abundance	1 na
7	NaN3	natural abundance	0.02 %
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

6 3D 1H-13C arom NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	YR313A.037	[U-100% 13C; U-100% 15N]	1.027 mM
2	NaCl	natural abundance	450 mM
3	Na2PO4	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	ZnSO4	natural abundance	20 uM
6	Proteinase inhibitors	natural abundance	1 na
7	NaN3	natural abundance	0.02 %
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

7 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	YR313A.037	[U-100% 13C; U-100% 15N]	1.027 mM
2	NaCl	natural abundance	450 mM
3	Na2PO4	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	ZnSO4	natural abundance	20 uM
6	Proteinase inhibitors	natural abundance	1 na
7	NaN3	natural abundance	0.02 %
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

8 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz at UGA

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.52 mM YR313A.037, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
10	YR313A.040	[U-10% 13C; U-100% 15N]	0.52 mM
11	NaCl	natural abundance	450 mM
12	Na2PO4	natural abundance	25 mM
13	DTT	natural abundance	10 mM
14	ZnSO4	natural abundance	20 uM
15	Proteinase inhibitors	natural abundance	1 na
16	NaN3	natural abundance	0.02 %
17	D2O	natural abundance	10 %
18	H2O	natural abundance	90 %

9 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 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	YR313A.037	[U-100% 13C; U-100% 15N]	1.027 mM
2	NaCl	natural abundance	450 mM
3	Na2PO4	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	ZnSO4	natural abundance	20 uM
6	Proteinase inhibitors	natural abundance	1 na
7	NaN3	natural abundance	0.02 %
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18487_2ltl.nef
Input source #2: Coordindates	2ltl.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
MGHHHHHHSHMNSQRLIHIKTLTTPNENALKFLSTDGEMLQTRGSKSIVIKNTDENLINHSKLAQQIFLQCPGVESLMIGDDFLTINKDRMVHWNSIKPE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHSHMNSQRLIHIKTLTTPNENALKFLSTDGEMLQTRGSKSIVIKNTDENLINHSKLAQQIFLQCPGVESLMIGDDFLTINKDRMVHWNSIKPE

-------110---------
IIDLLTKQLAYGEDVISKE
|||||||||||||||||||
IIDLLTKQLAYGEDVISKE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	119	0	0	100.0

Content subtype: combined_18487_2ltl.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1173		92.4 (chain: A, length: 119)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3357 (1)	noe	89.9 (chain: A, length: 119)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	40 (1)	hbond	26.9 (chain: A, length: 119)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	122 (122)	.	64.7 (chain: A, length: 119)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 92.4%
- Total number of assignments
  - ¹H chemical shifts: 668
  - ¹³C chemical shifts: 386
  - ¹⁵N chemical shifts: 119
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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	738	668	90.5
¹³C chemical shifts	548	386	70.4
¹⁵N chemical shifts	134	119	88.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	241	219	90.9
¹³C chemical shifts	238	109	45.8
¹⁵N chemical shifts	116	104	89.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	497	449	90.3
¹³C chemical shifts	310	277	89.4
¹⁵N chemical shifts	18	15	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	72	97.3
¹³C chemical shifts	74	72	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	27	60.0
¹³C chemical shifts	44	25	56.8
¹⁵N chemical shifts	1	1	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: 119, Sequence coverage: 89.9%
- Total number of restraints: 3348
- Weight of restraints: 1.0 (3348)
- Potential type of restraints: square-well-parabolic (3348)
- Range of distance target values: 2.19, 4.35 (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: 119, Sequence coverage: 26.9%
  - Total number of restraints: 40
  - Weight of restraints: 1.0 (40)
  - Potential type of restraints: square-well-parabolic (40)
  - Range of distance target values: 1.99, 2.99 (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: 119, Sequence coverage: 64.7%
- Total number of restraints: 122
- Total number of restraints per polymer type: 122
- Weight of restraints: 1.0 (122)
- Potential type of restraints: square-well-parabolic (122)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), PSI-Biology, Protein NMR, Protein Structure Initiative, Structural Genomics, Target YR313A

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Found 1 Document (0.736 seconds)

BMRB: 18487

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. YR313A, : 1 : 34 entities Detail

Interaction partners 1. YR313A, : 3 interactors Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 5 contents Detail