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BMRB: 15837

2K5I

NMR CHEMICAL SHIFT ASSIGNMENTS OF IRON(II) TRANSPORT PROTEIN A FROM CLOSTRIDIUM THERMOCELLUM , NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET VR131

Authors

LIU, G., WANG, H., FOOTE, E.L., JIANG, M., XIAO, R., SWAPNA, G., NAIR, R., EVERETT, J.K., ACTON, T.B., ROST, B., Montelione, G.T.

Assembly

IRON(II) TRANSPORT PROTEIN A

Entity

1. IRON(II) TRANSPORT PROTEIN A (polymer, Thiol state: all free), 324 monomers, 36469.66 Da Detail

MKLSRLVPGV PARIKRLEVS GELHEKLVGM GFVPGEEIEI VQVAPLGDPI VCKIGNRNIT LRKREADLIE VEVVGGELPL ILADDGTYEI TKLNGGRRFL FRMKNLGIES GKKIQVSGRR YYIEGREIDL GYGEATKIWV RRVSDAGEES HPQKLEHHHH HHMKLSRLVP GVPARIKRLE VSGELHEKLV GMGFVPGEEI EIVQVAPLGD PIVCKIGNRN ITLRKREADL IEVEVVGGEL PLILADDGTY EITKLNGGRR FLFRMKNLGI ESGKKIQVSG RRYYIEGREI DLGYGEATKI WVRRVSDAGE ESHPQKLEHH HHHH

Formula weight

36469.66 Da

Source organism

Acetivibrio thermocellus

Exptl. method

solution NMR

Refine. method

simulated annealing, distance geometry, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 62.0 %, Completeness: 54.7 %, Completeness (bb): 52.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	54.7 % (2086 of 3816)	58.5 % (1173 of 2004)	48.4 % (719 of 1486)	59.5 % (194 of 326)
Backbone	52.2 % (1001 of 1916)	60.4 % (406 of 672)	44.1 % (412 of 934)	59.0 % (183 of 310)
Sidechain	56.9 % (1243 of 2186)	57.0 % (759 of 1332)	56.6 % (474 of 838)	62.5 % (10 of 16)
Aromatic	42.9 % (91 of 212)	49.1 % (52 of 106)	35.6 % (37 of 104)	100.0 % (2 of 2)
Methyl	65.6 % (257 of 392)	65.8 % (129 of 196)	65.3 % (128 of 196)

1. IRON(II) TRANSPORT PROTEIN A

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NMR buffer pH 6.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.92 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
4	entity	[U-10% 13C; U-100% 15N]	0.65 mM
5	H2O	natural abundance	90 %
6	D2O	[U-100% 2H]	10 %

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: 0.24 ppm, Outliers: 2 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: 0.24 ppm, Outliers: 2 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: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K5I, Strand ID: A Detail

Release date

2008-08-21

Citation

NMR CHEMICAL SHIFT ASSIGNMENTS OF IRON(II) TRANSPORT PROTEIN A FROM CLOSTRIDIUM THERMOCELLUM , NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET VR131
LIU, G., XIAO, R., Montelione, G.
Not known

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 NMR buffer pH 6.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.92 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %

2 3D 1H-13C NOESY (aliph)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NMR buffer pH 6.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.92 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %

3 3D SIMULTANEOUS CN-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 NMR buffer pH 6.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.92 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %

4 4,3D GFT CABCACONHN

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NMR buffer pH 6.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.92 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %

5 4,3D GFT HNNCABCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NMR buffer pH 6.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.92 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %

6 4,3D GFT HABCABCONHN

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NMR buffer pH 6.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.92 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %

7 3D CCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NMR buffer pH 6.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.92 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %

8 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
4	entity	[U-10% 13C; U-100% 15N]	0.65 mM
5	H2O	natural abundance	90 %
6	D2O	[U-100% 2H]	10 %

9 3D 1H-13C NOESY (arom)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details NMR buffer pH 6.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.92 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15837_2k5i.nef
Input source #2: Coordindates	2k5i.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
MKLSRLVPGVPARIKRLEVSGELHEKLVGMGFVPGEEIEIVQVAPLGDPIVCKIGNRNITLRKREADLIEVEVVGGELPLILADDGTYEITKLNGGRRFL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKLSRLVPGVPARIKRLEVSGELHEKLVGMGFVPGEEIEIVQVAPLGDPIVCKIGNRNITLRKREADLIEVEVVGGELPLILADDGTYEITKLNGGRRFL

-------110-------120-------130-------140-------150-------160--
FRMKNLGIESGKKIQVSGRRYYIEGREIDLGYGEATKIWVRRVSDAGEESHPQKLEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
FRMKNLGIESGKKIQVSGRRYYIEGREIDLGYGEATKIWVRRVSDAGEESHPQKLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	162	0	0	100.0

Content subtype: combined_15837_2k5i.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1677		97.5 (chain: A, length: 162)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	6201 (1)	noe	97.5 (chain: A, length: 162)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	72 (1)	hbond	34.6 (chain: A, length: 162)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 162, Sequence coverage: 97.5%
- Total number of assignments
  - ¹H chemical shifts: 966
  - ¹³C chemical shifts: 547
  - ¹⁵N chemical shifts: 164
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
52	CYS	HG	1.67
136	THR	HG1	5.01

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1002	964	96.2
¹³C chemical shifts	743	547	73.6
¹⁵N chemical shifts	177	164	92.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	336	327	97.3
¹³C chemical shifts	324	158	48.8
¹⁵N chemical shifts	155	150	96.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	666	637	95.6
¹³C chemical shifts	419	389	92.8
¹⁵N chemical shifts	22	14	63.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	101	101	100.0
¹³C chemical shifts	101	101	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	40	75.5
¹³C chemical shifts	52	26	50.0
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: 162, Sequence coverage: 97.5%
- Total number of restraints: 6201
- Weight of restraints: 1.0 (6201)
- Potential type of restraints: square-well-parabolic (6201)
- Range of distance target values: 2.36, 4.8 (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_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 162, Sequence coverage: 34.6%
  - Total number of restraints: 72
  - Weight of restraints: 1.0 (72)
  - Potential type of restraints: square-well-parabolic (72)
  - Range of distance target values: 2.1, 2.7 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

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Found 1 Document (1.075 seconds)

BMRB: 15837

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Experiments performed 9 experiments Detail

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NMR combined restraints 4 contents Detail