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BMRB: 16091

2KCP

SOLUTION STRUCTURE OF 30S RIBOSOMAL PROTEIN S8E; FROM Methanothermobacter thermautotrophicus, NORTHEASTSTRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET TR71D

Authors

Liu, G., Rossi, P., Wang, D., NWOSU, C., OWENS, L., Xiao, R., Liu, J., BARAN, M.C., SWAPNA, G., ACTON, T.B., Rost, B., MONTELIONE, G.T.

Assembly

rps8

Entity

1. rps8 (polymer, Thiol state: all free), 294 monomers, 33018.84 Da Detail

GDRRVRLIRT RGGNTKVRLA SDTRINVVDP ETGKVEIAEI RNVVENTANP HFVRRNIITR GAVVETNLGN VRVTSRPGQD GVINGVLIRE LEHHHHHHGD RRVRLIRTRG GNTKVRLASD TRINVVDPET GKVEIAEIRN VVENTANPHF VRRNIITRGA VVETNLGNVR VTSRPGQDGV INGVLIRELE HHHHHHGDRR VRLIRTRGGN TKVRLASDTR INVVDPETGK VEIAEIRNVV ENTANPHFVR RNIITRGAVV ETNLGNVRVT SRPGQDGVIN GVLIRELEHH HHHH

Formula weight

33018.84 Da

Source organism

Methanothermobacter thermautotrophicus

Exptl. method

solution NMR

Refine. method

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

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 45.6 %, Completeness: 36.1 %, Completeness (bb): 35.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	36.1 % (1202 of 3330)	38.6 % (669 of 1734)	31.4 % (402 of 1281)	41.6 % (131 of 315)
Backbone	35.9 % (627 of 1746)	41.7 % (253 of 606)	29.6 % (253 of 855)	42.5 % (121 of 285)
Sidechain	36.7 % (679 of 1851)	36.9 % (416 of 1128)	36.5 % (253 of 693)	33.3 % (10 of 30)
Aromatic	6.1 % (7 of 114)	12.3 % (7 of 57)	0.0 % (0 of 57)
Methyl	41.2 % (163 of 396)	41.9 % (83 of 198)	40.4 % (80 of 198)

1. rps8e

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	rps8e	[U-100% 13C; U-100% 15N]	0.94 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
4	rps8e	[U-10% 13C; U-100% 15N]	1 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	rps8e	[U-100% 13C; U-100% 15N]		0.94 mM
8	D2O	natural abundance		100 %

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: 0.08 ppm, Outliers: 1 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: 0.08 ppm, Outliers: 1 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: 0.04 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2009-02-16

Citation

SOLUTION STRUCTURE OF 30S RIBOSOMAL PROTEIN S8E FROM Methanothermobacter thermautotrophicus, NORTHEASTSTRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET
Liu, G., MONTELIONE, G.
Not known

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz NYSBC

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	rps8e	[U-100% 13C; U-100% 15N]	0.94 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz NYSBC

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	rps8e	[U-100% 13C; U-100% 15N]	0.94 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

3 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz NYSBC

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	rps8e	[U-100% 13C; U-100% 15N]	0.94 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

4 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz NYSBC

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
4	rps8e	[U-10% 13C; U-100% 15N]	1 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz NYSBC

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	rps8e	[U-100% 13C; U-100% 15N]	0.94 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

6 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz NYSBC

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	rps8e	[U-100% 13C; U-100% 15N]	0.94 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

7 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz NYSBC

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	rps8e	[U-100% 13C; U-100% 15N]		0.94 mM
8	D2O	natural abundance		100 %

8 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	rps8e	[U-100% 13C; U-100% 15N]	0.94 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

9 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	rps8e	[U-100% 13C; U-100% 15N]	0.94 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

10 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	rps8e	[U-100% 13C; U-100% 15N]	0.94 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

11 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	rps8e	[U-100% 13C; U-100% 15N]	0.94 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

12 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	rps8e	[U-100% 13C; U-100% 15N]		0.94 mM
8	D2O	natural abundance		100 %

13 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
4	rps8e	[U-10% 13C; U-100% 15N]	1 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_16091_2kcp.nef
Input source #2: Coordindates	2kcp.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--------
GDRRVRLIRTRGGNTKVRLASDTRINVVDPETGKVEIAEIRNVVENTANPHFVRRNIITRGAVVETNLGNVRVTSRPGQDGVINGVLIRELEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GDRRVRLIRTRGGNTKVRLASDTRINVVDPETGKVEIAEIRNVVENTANPHFVRRNIITRGAVVETNLGNVRVTSRPGQDGVINGVLIRELEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	98	0	0	100.0

Content subtype: combined_16091_2kcp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	930		95.9 (chain: A, length: 98)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2513 (1)	noe	91.8 (chain: A, length: 98)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	88 (88)	.	46.9 (chain: A, length: 98)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	39 (39)	.	39.8 (chain: A, length: 98)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 95.9%
- Total number of assignments
  - ¹H chemical shifts: 530
  - ¹³C chemical shifts: 303
  - ¹⁵N chemical shifts: 97
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
66	THR	HG1	4.96

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	578	529	91.5
¹³C chemical shifts	427	303	71.0
¹⁵N chemical shifts	119	97	81.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	202	190	94.1
¹³C chemical shifts	196	94	48.0
¹⁵N chemical shifts	95	87	91.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	376	339	90.2
¹³C chemical shifts	231	209	90.5
¹⁵N chemical shifts	24	10	41.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	66	100.0
¹³C chemical shifts	66	66	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	3	15.8
¹³C chemical shifts	19	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 91.8%
- Total number of restraints: 2513
- Weight of restraints: 1.0 (2513)
- Potential type of restraints: square-well-parabolic (2513)
- Range of distance target values: 2.05, 4.64 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 46.9%
- Total number of restraints: 88
- Total number of restraints per polymer type: 88
- Weight of restraints: 1.0 (88)
- Potential type of restraints: square-well-parabolic (88)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 39.8%
- Total number of restraints: 39
- Potential type of restraints: undefined (39)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords 30S RIBOSOMAL PROTEIN S8E, NESG, rps8e

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BMRB: 16091

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Chemical shift reference

Chemical shift reference

Experiments performed 13 experiments Detail

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NMR combined restraints 5 contents Detail