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BMRB: 19860

2MMP

Solution structure of a ribosomal protein

Authors

Assembly

a ribosomal protein

Entity

1. a ribosomal protein (polymer, Thiol state: not present), 77 monomers, 9200.613 Da Detail

MLKHGKYVYI DLNNGKYVKV RILKSRDDNS VEKYVLTSHV SKNRPKNAIV IKMDNLPIEV KDKLTRFFLL EHHHHHH

Formula weight

9200.613 Da

Source organism

Saccharolobus solfataricus

Exptl. method

Refine. method

molecular dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.7 %, Completeness: 95.4 %, Completeness (bb): 98.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.4 % (926 of 971)	95.5 % (487 of 510)	94.7 % (360 of 380)	97.5 % (79 of 81)
Backbone	98.3 % (450 of 458)	98.1 % (151 of 154)	98.7 % (226 of 229)	97.3 % (73 of 75)
Sidechain	93.5 % (550 of 588)	94.4 % (336 of 356)	92.0 % (208 of 226)	100.0 % (6 of 6)
Aromatic	65.5 % (55 of 84)	66.7 % (28 of 42)	64.3 % (27 of 42)
Methyl	100.0 % (90 of 90)	100.0 % (45 of 45)	100.0 % (45 of 45)

1. rib prot

MLKHGKYVYI DLNNGKYVKV RILKSRDDNS VEKYVLTSHV SKNRPKNAIV IKMDNLPIEV KDKLTRFFLL EHHHHHH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	rib_prot	[U-13C; U-15N]		0.5 ~ 1.0 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		50 mM
4	EDTA	natural abundance		2 mM
5	DSS	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

LACS Plot; CA

Referencing offset: -0.32 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.32 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.08 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.16 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2014-06-08

Citation

Structure determination of archaea-specific ribosomal protein L46a reveals a novel protein fold
Feng, Y., Song, X., Lin, J., Xuan, J., Cui, Q., Wang, J.
Biochem. Biophys. Res. Commun. (2014), 450, 67-72, PubMed 24875358 , DOI 10.1016/j.bbrc.2014.05.077 , Abstract

Related entities 1. a ribosomal protein, : 1 : 14 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	rib_prot	[U-13C; U-15N]		0.5 ~ 1.0 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		50 mM
4	EDTA	natural abundance		2 mM
5	DSS	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

2 2D 1H-13C HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	rib_prot	[U-13C; U-15N]		0.5 ~ 1.0 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		50 mM
4	EDTA	natural abundance		2 mM
5	DSS	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

3 3D HNCO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	rib_prot	[U-13C; U-15N]		0.5 ~ 1.0 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		50 mM
4	EDTA	natural abundance		2 mM
5	DSS	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

4 3D HNCACB

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	rib_prot	[U-13C; U-15N]		0.5 ~ 1.0 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		50 mM
4	EDTA	natural abundance		2 mM
5	DSS	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

5 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	rib_prot	[U-13C; U-15N]		0.5 ~ 1.0 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		50 mM
4	EDTA	natural abundance		2 mM
5	DSS	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

6 3D HN(CA)CO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	rib_prot	[U-13C; U-15N]		0.5 ~ 1.0 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		50 mM
4	EDTA	natural abundance		2 mM
5	DSS	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

7 3D HBHA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	rib_prot	[U-13C; U-15N]		0.5 ~ 1.0 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		50 mM
4	EDTA	natural abundance		2 mM
5	DSS	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

8 3D HBHANH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	rib_prot	[U-13C; U-15N]		0.5 ~ 1.0 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		50 mM
4	EDTA	natural abundance		2 mM
5	DSS	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

9 3D CCH-TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	rib_prot	[U-13C; U-15N]		0.5 ~ 1.0 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		50 mM
4	EDTA	natural abundance		2 mM
5	DSS	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

10 3D 1H-15N TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	rib_prot	[U-13C; U-15N]		0.5 ~ 1.0 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		50 mM
4	EDTA	natural abundance		2 mM
5	DSS	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

11 3D 1H-15N NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	rib_prot	[U-13C; U-15N]		0.5 ~ 1.0 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		50 mM
4	EDTA	natural abundance		2 mM
5	DSS	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

12 3D 1H-13C NOESY aliphatic

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	rib_prot	[U-13C; U-15N]		0.5 ~ 1.0 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		50 mM
4	EDTA	natural abundance		2 mM
5	DSS	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

13 3D 1H-13C NOESY aromatic

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	rib_prot	[U-13C; U-15N]		0.5 ~ 1.0 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		50 mM
4	EDTA	natural abundance		2 mM
5	DSS	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19860_2mmp.nef
Input source #2: Coordindates	2mmp.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-------
MLKHGKYVYIDLNNGKYVKVRILKSRDDNSVEKYVLTSHVSKNRPKNAIVIKMDNLPIEVKDKLTRFFLLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MLKHGKYVYIDLNNGKYVKVRILKSRDDNSVEKYVLTSHVSKNRPKNAIVIKMDNLPIEVKDKLTRFFLLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	77	0	0	100.0

Content subtype: combined_19860_2mmp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	930		98.7 (chain: A, length: 77)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3828 (1)	noe	98.7 (chain: A, length: 77)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	50 (1)	hbond	46.8 (chain: A, length: 77)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	116 (116)	.	83.1 (chain: A, length: 77)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 77, Sequence coverage: 98.7%
- Total number of assignments
  - ¹H chemical shifts: 487
  - ¹³C chemical shifts: 360
  - ¹⁵N chemical shifts: 83
- 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_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 77, Sequence coverage: 98.7%
- Total number of restraints: 3826
- Weight of restraints: 1.0 (3826)
- Potential type of restraints: square-well-parabolic (3826)
- Range of distance target values: 2.3, 4.15 (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
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 77, Sequence coverage: 46.8%
  - Total number of restraints: 50
  - Weight of restraints: 1.0 (50)
  - Potential type of restraints: square-well-parabolic (50)
  - Range of distance target values: 2.0, 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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 77, Sequence coverage: 83.1%
- Total number of restraints: 116
- Total number of restraints per polymer type: 116
- Weight of restraints: 1.0 (116)
- Potential type of restraints: square-well-parabolic (116)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Ribosomal protein