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BMRB: 18290

2LQ3

Solution NMR Structure of syc0711_d from Synechococcus sp., Northeast Structural Genomics Consortium (NESG) Target SnR212

Authors

Mills, J.L., Sathymoorthy, B., Pulavarti, S., Janjua, H., Kohan, E., Wang, D., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Szyperski, T.

Assembly

SnR212

Entity

1. SnR212 (polymer, Thiol state: all free), 130 monomers, 14641.39 Da Detail

MGQGQNVLGQ DLEVCCCAPM TGWYRNGFCQ TDVQDRGSHT VCAEMTEEFL LFSRDRGNDL MTPRPEFNFP GLKAGDRWCL CASRWQEAFE AGMAPPVVLQ STEKSALRYV SLADLQAHAL PVLEHHHHHH

Formula weight

14641.39 Da

Source organism

Synechococcus sp.

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.5 %, Completeness: 79.3 %, Completeness (bb): 87.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.3 % (1170 of 1475)	78.5 % (600 of 764)	78.7 % (451 of 573)	86.2 % (119 of 138)
Backbone	87.1 % (667 of 766)	86.7 % (228 of 263)	86.8 % (330 of 380)	88.6 % (109 of 123)
Sidechain	73.6 % (610 of 829)	74.3 % (372 of 501)	72.8 % (228 of 313)	66.7 % (10 of 15)
Aromatic	33.3 % (48 of 144)	38.9 % (28 of 72)	24.6 % (17 of 69)	100.0 % (3 of 3)
Methyl	90.7 % (107 of 118)	93.2 % (55 of 59)	88.1 % (52 of 59)

1. SnR212

MGQGQNVLGQ DLEVCCCAPM TGWYRNGFCQ TDVQDRGSHT VCAEMTEEFL LFSRDRGNDL MTPRPEFNFP GLKAGDRWCL CASRWQEAFE AGMAPPVVLQ STEKSALRYV SLADLQAHAL PVLEHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.89 mM SnR212.015, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	SnR212.015	[U-100% 13C; U-100% 15N]	0.89 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM
10	H2O	natural abundance	90 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.67 mM SnR212.015, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	SnR212.015	[U-100% 13C; U-100% 15N]	0.67 mM
12	NaN3	natural abundance	0.02 %
13	DTT	natural abundance	10 mM
14	CaCL2	natural abundance	5 mM
15	NaCL	natural abundance	100 mM
16	Proteinase Inhibitors	natural abundance	1 na
17	MES pH 6.5	natural abundance	20 mM
18	D2O	natural abundance	10 %
19	DSS	natural abundance	50 uM
20	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: -0.01 ppm, Outliers: 2 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: -0.01 ppm, Outliers: 2 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: 0.06 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: 0.03 ppm, Outliers: 6 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LQ3, Strand ID: A Detail

Release date

2012-03-21

Related entities 1. SnR212, : 1 : 2 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.89 mM SnR212.015, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	SnR212.015	[U-100% 13C; U-100% 15N]	0.89 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM
10	H2O	natural abundance	90 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.89 mM SnR212.015, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	SnR212.015	[U-100% 13C; U-100% 15N]	0.89 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM
10	H2O	natural abundance	90 %

3 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.89 mM SnR212.015, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	SnR212.015	[U-100% 13C; U-100% 15N]	0.89 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM
10	H2O	natural abundance	90 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.89 mM SnR212.015, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	SnR212.015	[U-100% 13C; U-100% 15N]	0.89 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM
10	H2O	natural abundance	90 %

5 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.89 mM SnR212.015, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	SnR212.015	[U-100% 13C; U-100% 15N]	0.89 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM
10	H2O	natural abundance	90 %

6 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.89 mM SnR212.015, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	SnR212.015	[U-100% 13C; U-100% 15N]	0.89 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM
10	H2O	natural abundance	90 %

7 2D 1H-13C HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.67 mM SnR212.015, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	SnR212.015	[U-100% 13C; U-100% 15N]	0.67 mM
12	NaN3	natural abundance	0.02 %
13	DTT	natural abundance	10 mM
14	CaCL2	natural abundance	5 mM
15	NaCL	natural abundance	100 mM
16	Proteinase Inhibitors	natural abundance	1 na
17	MES pH 6.5	natural abundance	20 mM
18	D2O	natural abundance	10 %
19	DSS	natural abundance	50 uM
20	H2O	natural abundance	90 %

8 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.89 mM SnR212.015, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	SnR212.015	[U-100% 13C; U-100% 15N]	0.89 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM
10	H2O	natural abundance	90 %

9 3D HCCH-COSY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.89 mM SnR212.015, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	SnR212.015	[U-100% 13C; U-100% 15N]	0.89 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM
10	H2O	natural abundance	90 %

10 3D HNCA

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.89 mM SnR212.015, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	SnR212.015	[U-100% 13C; U-100% 15N]	0.89 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM
10	H2O	natural abundance	90 %

11 3D HN(CO)CA

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.89 mM SnR212.015, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	SnR212.015	[U-100% 13C; U-100% 15N]	0.89 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM
10	H2O	natural abundance	90 %

12 3D HN(CA)CO

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.89 mM SnR212.015, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	SnR212.015	[U-100% 13C; U-100% 15N]	0.89 mM
2	NaN3	natural abundance	0.02 %
3	DTT	natural abundance	10 mM
4	CaCL2	natural abundance	5 mM
5	NaCL	natural abundance	100 mM
6	Proteinase Inhibitors	natural abundance	1 na
7	MES pH 6.5	natural abundance	20 mM
8	D2O	natural abundance	10 %
9	DSS	natural abundance	50 uM
10	H2O	natural abundance	90 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18290_2lq3.nef
Input source #2: Coordindates	2lq3.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
MGQGQNVLGQDLEVCCCAPMTGWYRNGFCQTDVQDRGSHTVCAEMTEEFLLFSRDRGNDLMTPRPEFNFPGLKAGDRWCLCASRWQEAFEAGMAPPVVLQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGQGQNVLGQDLEVCCCAPMTGWYRNGFCQTDVQDRGSHTVCAEMTEEFLLFSRDRGNDLMTPRPEFNFPGLKAGDRWCLCASRWQEAFEAGMAPPVVLQ

-------110-------120-------130
STEKSALRYVSLADLQAHALPVLEHHHHHH
||||||||||||||||||||||||||||||
STEKSALRYVSLADLQAHALPVLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	130	0	0	100.0

Content subtype: combined_18290_2lq3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1161		90.8 (chain: A, length: 130)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	2606 (1)	noe	90.0 (chain: A, length: 130)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	84 (84)	.	43.8 (chain: A, length: 130)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 130, Sequence coverage: 90.8%
- Total number of assignments
  - ¹H chemical shifts: 601
  - ¹³C chemical shifts: 445
  - ¹⁵N chemical shifts: 115
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	764	601	78.7
¹³C chemical shifts	573	445	77.7
¹⁵N chemical shifts	146	115	78.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	263	228	86.7
¹³C chemical shifts	260	219	84.2
¹⁵N chemical shifts	123	105	85.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	501	373	74.5
¹³C chemical shifts	313	226	72.2
¹⁵N chemical shifts	23	10	43.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	64	59	92.2
¹³C chemical shifts	64	55	85.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	28	38.9
¹³C chemical shifts	69	17	24.6
¹⁵N chemical shifts	3	3	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 130, Sequence coverage: 90.0%
- Total number of restraints: 2604
- Weight of restraints: 1.0 (2604)
- Potential type of restraints: square-well-parabolic (2604)
- Range of distance target values: 1.27, 3.15 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 130, Sequence coverage: 43.8%
- Total number of restraints: 84
- Total number of restraints per polymer type: 84
- Weight of restraints: 1.0 (84)
- Potential type of restraints: square-well-parabolic (84)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), Protein NMR, Protein Structure Initiative, PSI:Biology, Structural Genomics, Target SnR212

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Found 1 Document (0.6 seconds)

BMRB: 18290

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. SnR212, : 1 : 2 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 4 contents Detail