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BMRB: 16240

2KFW

Solution structure of full-length SlyD from E.coli

Authors

Martino, L., Kelly, G., Conte, M.R.

Assembly

SlyD

Entity

1. SlyD (polymer, Thiol state: all free), 196 monomers, 20852.60 Da Detail

MKVAKDLVVS LAYQVRTEDG VLVDESPVSA PLDYLHGHGS LISGLETALE GHEVGDKFDV AVGANDAYGQ YDENLVQRVP KDVFMGVDEL QVGMRFLAET DQGPVPVEIT AVEDDHVVVD GNHMLAGQNL KFNVEVVAIR EATEEELAHG HVHGAHDHHH DHDHDGCCGG HGHDHGHEHG GEGCCGGKGN GGCGCH

Formula weight

20852.6 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 83.2 %, Completeness: 74.4 %, Completeness (bb): 79.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.4 % (1530 of 2057)	72.4 % (757 of 1046)	76.5 % (618 of 808)	76.4 % (155 of 203)
Backbone	79.3 % (925 of 1166)	77.9 % (324 of 416)	80.1 % (448 of 559)	80.1 % (153 of 191)
Sidechain	70.4 % (745 of 1058)	68.7 % (433 of 630)	74.5 % (310 of 416)	16.7 % (2 of 12)
Aromatic	36.8 % (56 of 152)	38.2 % (29 of 76)	35.5 % (27 of 76)
Methyl	88.8 % (183 of 206)	89.3 % (92 of 103)	88.3 % (91 of 103)

1. SlyD

MKVAKDLVVS LAYQVRTEDG VLVDESPVSA PLDYLHGHGS LISGLETALE GHEVGDKFDV AVGANDAYGQ YDENLVQRVP KDVFMGVDEL QVGMRFLAET DQGPVPVEIT AVEDDHVVVD GNHMLAGQNL KFNVEVVAIR EATEEELAHG HVHGAHDHHH DHDHDGCCGG HGHDHGHEHG GEGCCGGKGN GGCGCH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 ~ 0.9 mM
2	TRIS	natural abundance		20 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM

LACS Plot; CA

Referencing offset: -0.03 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.03 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.0 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.3 ppm, Outliers: 5 Detail

Protein Blocks Logo

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

Release date

2009-09-23

Citation

Letter to the Editor: resonance assignment of SlyD from E. coli
Martino, L., Kelly, G., Conte, M.R.
Biomol. NMR Assign. (2009), 3, 235-237, PubMed 19760519 , DOI 10.1007/s12104-009-9183-3 , Abstract

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

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 ~ 0.9 mM
2	TRIS	natural abundance		20 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 ~ 0.9 mM
2	TRIS	natural abundance		20 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM

3 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 ~ 0.9 mM
2	TRIS	natural abundance		20 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM

4 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 ~ 0.9 mM
2	TRIS	natural abundance		20 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM

5 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 ~ 0.9 mM
2	TRIS	natural abundance		20 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM

6 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 ~ 0.9 mM
2	TRIS	natural abundance		20 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 ~ 0.9 mM
2	TRIS	natural abundance		20 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM

8 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 ~ 0.9 mM
2	TRIS	natural abundance		20 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 ~ 0.9 mM
2	TRIS	natural abundance		20 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM

10 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 ~ 0.9 mM
2	TRIS	natural abundance		20 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM

11 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 ~ 0.9 mM
2	TRIS	natural abundance		20 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM

12 3D HN(CO)CA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 ~ 0.9 mM
2	TRIS	natural abundance		20 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16240_2kfw.nef
Input source #2: Coordindates	2kfw.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
MKVAKDLVVSLAYQVRTEDGVLVDESPVSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENLVQRVPKDVFMGVDELQVGMRFLAET
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKVAKDLVVSLAYQVRTEDGVLVDESPVSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENLVQRVPKDVFMGVDELQVGMRFLAET

-------110-------120-------130-------140-------150-------160-------170-------180-------190------
DQGPVPVEITAVEDDHVVVDGNHMLAGQNLKFNVEVVAIREATEEELAHGHVHGAHDHHHDHDHDGCCGGHGHDHGHEHGGEGCCGGKGNGGCGCH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
DQGPVPVEITAVEDDHVVVDGNHMLAGQNLKFNVEVVAIREATEEELAHGHVHGAHDHHHDHDHDGCCGGHGHDHGHEHGGEGCCGGKGNGGCGCH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	196	0	0	100.0

Content subtype: combined_16240_2kfw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1489		80.1 (chain: A, length: 196)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	2081 (1)	noe	79.1 (chain: A, length: 196)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	46 (1)	hbond	13.3 (chain: A, length: 196)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	227 (227)	.	73.5 (chain: A, length: 196)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 196, Sequence coverage: 80.1%
- Total number of assignments
  - ¹H chemical shifts: 732
  - ¹³C chemical shifts: 609
  - ¹⁵N chemical shifts: 148
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 196, Sequence coverage: 79.1%
- Total number of restraints: 2080
- Weight of restraints: 1.0 (2080)
- Potential type of restraints: square-well-parabolic (2080)
- Range of distance target values: 2.3, 3.65 (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: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 196, Sequence coverage: 13.3%
  - Total number of restraints: 46
  - Weight of restraints: 1.0 (46)
  - Potential type of restraints: square-well-parabolic (46)
  - Range of distance target values: 2.1, 3.0 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 196, Sequence coverage: 73.5%
- Total number of restraints: 227
- Total number of restraints per polymer type: 227
- Weight of restraints: 1.0 (227)
- Potential type of restraints: square-well-parabolic (227)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Protein, SlyD