BMRBj - BMREntryMaster

Found 1 Document (0.597 seconds)

BMRB: 16388

2KLB

NMR Solution structure of a diflavin flavoprotein A3 from Nostoc sp. PCC 7120, Northeast Structural Genomics Consortium Target NsR431C

Authors

Swapna, G., Ciccosanti, C., Wang, D., Jiang, M., Xiao, R., Acton, T., Everett, J., Nair, R., Montelione, G.

Assembly

NsR431C

Entity

1. NsR431C (polymer, Thiol state: not present), 154 monomers, 16457.33 Da Detail

SIGVFYVSEY GYSDRLAQAI INGITKTGVG VDVVDLGAAV DLQELRELVG RCTGLVIGMS PAASAASIQG ALSTILGSVN EKQAVGIFET GGGDDEPIDP LLSKFRNLGL TTAFPAIRIK QTPTENTYKL CEEAGTDLGQ WVTRDRLEHH HHHH

Formula weight

16457.33 Da

Source organism

Nostoc sp. PCC 7120 = FACHB-418

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 93.3 %, Completeness (bb): 94.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.3 % (1579 of 1692)	93.3 % (806 of 864)	92.5 % (618 of 668)	96.9 % (155 of 160)
Backbone	94.7 % (866 of 914)	96.0 % (308 of 321)	93.5 % (415 of 444)	96.0 % (143 of 149)
Sidechain	91.4 % (835 of 914)	90.6 % (492 of 543)	92.2 % (332 of 360)	100.0 % (11 of 11)
Aromatic	72.2 % (78 of 108)	72.2 % (39 of 54)	71.7 % (38 of 53)	100.0 % (1 of 1)
Methyl	100.0 % (202 of 202)	100.0 % (101 of 101)	100.0 % (101 of 101)

1. NsR431C

SIGVFYVSEY GYSDRLAQAI INGITKTGVG VDVVDLGAAV DLQELRELVG RCTGLVIGMS PAASAASIQG ALSTILGSVN EKQAVGIFET GGGDDEPIDP LLSKFRNLGL TTAFPAIRIK QTPTENTYKL CEEAGTDLGQ WVTRDRLEHH HHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 1.18mM NsR431C, 10mM DTT, 50uM DSS, 0.02% NaN3,200mM NaCl, 5mM CaCl2, 20mM MES, protease inhibitors added.

#	Name	Isotope labeling	Concentration
1	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
2	DTT	natural abundance	10 mM
3	DSS	natural abundance	50 uM
4	NaN3	natural abundance	0.02 %
5	NaCl	natural abundance	200 mM
6	CaCl2	natural abundance	5 mM
7	MES	natural abundance	20 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 1.18mM NsR431C, 10mM DTT, 50uM DSS, 0.02% NaN3,200mM NaCl, 5mM CaCl2, 20mM MES, protease inhibitors added.

#	Name	Isotope labeling	Concentration
10	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
11	DTT	natural abundance	10 mM
12	DSS	natural abundance	50 uM
13	NaN3	natural abundance	0.02 %
14	NaCl	natural abundance	200 mM
15	CaCl2	natural abundance	5 mM
16	MES	natural abundance	20 mM
17	D2O	natural abundance	100 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 1.18mM NsR431C, 10mM DTT, 50uM DSS, 0.02% NaN3,200mM NaCl, 5mM CaCl2, 20mM MES, protease inhibitors added.

#	Name	Isotope labeling	Concentration
18	NsR431C	[U-10% 13C; U-100% 15N]	1.18 (±0.2) mM
19	DTT	natural abundance	10 mM
20	DSS	natural abundance	50 uM
21	NaN3	natural abundance	0.02 %
22	NaCl	natural abundance	200 mM
23	CaCl2	natural abundance	5 mM
24	MES	natural abundance	20 mM
25	D2O	natural abundance	100 %

LACS Plot; CA

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

Referencing offset: -0.41 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.41 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.09 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 2.79 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2009-08-05

Related entities 1. NsR431C, : 1 : 2 : 20 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 1.18mM NsR431C, 10mM DTT, 50uM DSS, 0.02% NaN3,200mM NaCl, 5mM CaCl2, 20mM MES, protease inhibitors added.

#	Name	Isotope labeling	Concentration
1	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
2	DTT	natural abundance	10 mM
3	DSS	natural abundance	50 uM
4	NaN3	natural abundance	0.02 %
5	NaCl	natural abundance	200 mM
6	CaCl2	natural abundance	5 mM
7	MES	natural abundance	20 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
2	DTT	natural abundance	10 mM
3	DSS	natural abundance	50 uM
4	NaN3	natural abundance	0.02 %
5	NaCl	natural abundance	200 mM
6	CaCl2	natural abundance	5 mM
7	MES	natural abundance	20 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
2	DTT	natural abundance	10 mM
3	DSS	natural abundance	50 uM
4	NaN3	natural abundance	0.02 %
5	NaCl	natural abundance	200 mM
6	CaCl2	natural abundance	5 mM
7	MES	natural abundance	20 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
2	DTT	natural abundance	10 mM
3	DSS	natural abundance	50 uM
4	NaN3	natural abundance	0.02 %
5	NaCl	natural abundance	200 mM
6	CaCl2	natural abundance	5 mM
7	MES	natural abundance	20 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

5 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
2	DTT	natural abundance	10 mM
3	DSS	natural abundance	50 uM
4	NaN3	natural abundance	0.02 %
5	NaCl	natural abundance	200 mM
6	CaCl2	natural abundance	5 mM
7	MES	natural abundance	20 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

6 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
2	DTT	natural abundance	10 mM
3	DSS	natural abundance	50 uM
4	NaN3	natural abundance	0.02 %
5	NaCl	natural abundance	200 mM
6	CaCl2	natural abundance	5 mM
7	MES	natural abundance	20 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

7 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
2	DTT	natural abundance	10 mM
3	DSS	natural abundance	50 uM
4	NaN3	natural abundance	0.02 %
5	NaCl	natural abundance	200 mM
6	CaCl2	natural abundance	5 mM
7	MES	natural abundance	20 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
2	DTT	natural abundance	10 mM
3	DSS	natural abundance	50 uM
4	NaN3	natural abundance	0.02 %
5	NaCl	natural abundance	200 mM
6	CaCl2	natural abundance	5 mM
7	MES	natural abundance	20 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
2	DTT	natural abundance	10 mM
3	DSS	natural abundance	50 uM
4	NaN3	natural abundance	0.02 %
5	NaCl	natural abundance	200 mM
6	CaCl2	natural abundance	5 mM
7	MES	natural abundance	20 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
2	DTT	natural abundance	10 mM
3	DSS	natural abundance	50 uM
4	NaN3	natural abundance	0.02 %
5	NaCl	natural abundance	200 mM
6	CaCl2	natural abundance	5 mM
7	MES	natural abundance	20 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

11 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 1.18mM NsR431C, 10mM DTT, 50uM DSS, 0.02% NaN3,200mM NaCl, 5mM CaCl2, 20mM MES, protease inhibitors added.

#	Name	Isotope labeling	Concentration
18	NsR431C	[U-10% 13C; U-100% 15N]	1.18 (±0.2) mM
19	DTT	natural abundance	10 mM
20	DSS	natural abundance	50 uM
21	NaN3	natural abundance	0.02 %
22	NaCl	natural abundance	200 mM
23	CaCl2	natural abundance	5 mM
24	MES	natural abundance	20 mM
25	D2O	natural abundance	100 %

12 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
18	NsR431C	[U-10% 13C; U-100% 15N]	1.18 (±0.2) mM
19	DTT	natural abundance	10 mM
20	DSS	natural abundance	50 uM
21	NaN3	natural abundance	0.02 %
22	NaCl	natural abundance	200 mM
23	CaCl2	natural abundance	5 mM
24	MES	natural abundance	20 mM
25	D2O	natural abundance	100 %

13 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
10	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
11	DTT	natural abundance	10 mM
12	DSS	natural abundance	50 uM
13	NaN3	natural abundance	0.02 %
14	NaCl	natural abundance	200 mM
15	CaCl2	natural abundance	5 mM
16	MES	natural abundance	20 mM
17	D2O	natural abundance	100 %

14 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
10	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
11	DTT	natural abundance	10 mM
12	DSS	natural abundance	50 uM
13	NaN3	natural abundance	0.02 %
14	NaCl	natural abundance	200 mM
15	CaCl2	natural abundance	5 mM
16	MES	natural abundance	20 mM
17	D2O	natural abundance	100 %

15 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
10	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
11	DTT	natural abundance	10 mM
12	DSS	natural abundance	50 uM
13	NaN3	natural abundance	0.02 %
14	NaCl	natural abundance	200 mM
15	CaCl2	natural abundance	5 mM
16	MES	natural abundance	20 mM
17	D2O	natural abundance	100 %

16 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NsR431C	[U-100% 13C; U-100% 15N]	1.18 (±0.2) mM
2	DTT	natural abundance	10 mM
3	DSS	natural abundance	50 uM
4	NaN3	natural abundance	0.02 %
5	NaCl	natural abundance	200 mM
6	CaCl2	natural abundance	5 mM
7	MES	natural abundance	20 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16388_2klb.nef
Input source #2: Coordindates	2klb.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
SIGVFYVSEYGYSDRLAQAIINGITKTGVGVDVVDLGAAVDLQELRELVGRCTGLVIGMSPAASAASIQGALSTILGSVNEKQAVGIFETGGGDDEPIDP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SIGVFYVSEYGYSDRLAQAIINGITKTGVGVDVVDLGAAVDLQELRELVGRCTGLVIGMSPAASAASIQGALSTILGSVNEKQAVGIFETGGGDDEPIDP

-------110-------120-------130-------140-------150----
LLSKFRNLGLTTAFPAIRIKQTPTENTYKLCEEAGTDLGQWVTRDRLEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||
LLSKFRNLGLTTAFPAIRIKQTPTENTYKLCEEAGTDLGQWVTRDRLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	154	0	0	100.0

Content subtype: combined_16388_2klb.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1576		97.4 (chain: A, length: 154)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3398 (1)	noe	97.4 (chain: A, length: 154)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 154, Sequence coverage: 97.4%
- Total number of assignments
  - ¹H chemical shifts: 810
  - ¹³C chemical shifts: 612
  - ¹⁵N chemical shifts: 154
- 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	864	810	93.8
¹³C chemical shifts	668	612	91.6
¹⁵N chemical shifts	167	154	92.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	321	309	96.3
¹³C chemical shifts	308	280	90.9
¹⁵N chemical shifts	149	142	95.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	543	501	92.3
¹³C chemical shifts	360	332	92.2
¹⁵N chemical shifts	18	12	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	102	102	100.0
¹³C chemical shifts	102	102	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	39	72.2
¹³C chemical shifts	53	38	71.7
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: 154, Sequence coverage: 97.4%
- Total number of restraints: 3397
- Weight of restraints: 1.0 (3397)
- Potential type of restraints: square-well-parabolic (3397)
- Range of distance target values: 3.22, 4.9 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords diflavin flavoprotein, Northeast Structural Genomics Consortium, NsR431C, Protein NMR, Protein Structure Initiative, PSI-2, Q8YQD8

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Found 1 Document (0.597 seconds)

BMRB: 16388

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. NsR431C, : 1 : 2 : 20 entities Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 3 contents Detail