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Found 1 Document (0.642 seconds)

BMRB: 15609

2JZ6

solution structure of 50S ribosomal protein L28 from Thermotoga maritima: Northeast Structural Genomics consortium target VR97

Authors

Wu, Y., Singarapu, K., Guido, V., Yee, A., Sukumaran, D., Arrowsmith, C., Szyperski, T.

Assembly

ribosomal protein L28

Entity

1. ribosomal protein L28 (polymer, Thiol state: all free), 77 monomers, 8590.025 Da Detail

QGHMIMAKRC EVCGKAPRSG NTVSHSDKKS ERWFRPNLQK VRVVLPDGTI KRMRVCTSCL KSGKVKKYVG QVSEVGS

Formula weight

8590.025 Da

Source organism

Thermotoga maritima

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 81.8 %, Completeness: 74.8 %, Completeness (bb): 69.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.8 % (673 of 900)	80.5 % (385 of 478)	65.8 % (225 of 342)	78.8 % (63 of 80)
Backbone	69.1 % (315 of 456)	81.0 % (128 of 158)	57.1 % (128 of 224)	79.7 % (59 of 74)
Sidechain	81.1 % (417 of 514)	80.6 % (258 of 320)	82.4 % (155 of 188)	66.7 % (4 of 6)
Aromatic	68.4 % (26 of 38)	78.9 % (15 of 19)	55.6 % (10 of 18)	100.0 % (1 of 1)
Methyl	94.3 % (66 of 70)	94.3 % (33 of 35)	94.3 % (33 of 35)

1. ribosomal protein L28

QGHMIMAKRC EVCGKAPRSG NTVSHSDKKS ERWFRPNLQK VRVVLPDGTI KRMRVCTSCL KSGKVKKYVG QVSEVGS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	entity	natural abundance	1.0 mM
2	NaCl	natural abundance	300 mM
3	D2O	[U-100% 2H]	10 %
4	H2O		90 %

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
³¹P	DSS	methyl protons	null	indirect	0.4048086

Referencing offset: 0.02 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
³¹P	DSS	methyl protons	null	indirect	0.4048086

Referencing offset: 0.02 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
³¹P	DSS	methyl protons	null	indirect	0.4048086

Referencing offset: -0.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JZ6, Strand ID: A Detail

Release date

2008-01-24

Citation

solution structure of 50S ribosomal protein L28 from Thermotoga maritima: Northeast Structural Genomics consortium target VR97
Wu, Y., Singarapu, K., Guido, V., Yee, A., Sukumaran, D., Arrowsmith, C., Szyperski, T.

Related entities 1. ribosomal protein L28, : 1 : 1 : 173 entities Detail

Experiments performed 7 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15609_2jz6.nef
Input source #2: Coordindates	2jz6.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-------
QGHMIMAKRCEVCGKAPRSGNTVSHSDKKSERWFRPNLQKVRVVLPDGTIKRMRVCTSCLKSGKVKKYVGQVSEVGS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QGHMIMAKRCEVCGKAPRSGNTVSHSDKKSERWFRPNLQKVRVVLPDGTIKRMRVCTSCLKSGKVKKYVGQVSEVGS

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_15609_2jz6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	645		77.9 (chain: A, length: 77)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	926 (1)	noe	66.2 (chain: A, length: 77)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	179 (179)	.	90.9 (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: 77.9%
- Total number of assignments
  - ¹H chemical shifts: 374
  - ¹³C chemical shifts: 210
  - ¹⁵N chemical shifts: 61
- 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	478	374	78.2
¹³C chemical shifts	342	210	61.4
¹⁵N chemical shifts	87	61	70.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	158	122	77.2
¹³C chemical shifts	154	60	39.0
¹⁵N chemical shifts	74	57	77.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	320	252	78.7
¹³C chemical shifts	188	150	79.8
¹⁵N chemical shifts	13	4	30.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	33	86.8
¹³C chemical shifts	38	33	86.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	15	78.9
¹³C chemical shifts	18	10	55.6
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: 77, Sequence coverage: 66.2%
- Total number of restraints: 926
- Weight of restraints: 1.0 (926)
- Potential type of restraints: square-well-parabolic (926)
- Range of distance target values: 2.21, 5.69 (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: 77, Sequence coverage: 90.9%
- Total number of restraints: 179
- Total number of restraints per polymer type: 179
- Weight of restraints: 1.0 (179)
- Potential type of restraints: square-well-parabolic (179)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NESG, NMR, solution structure

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Found 1 Document (0.642 seconds)

BMRB: 15609

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. ribosomal protein L28, : 1 : 1 : 173 entities Detail

Experiments performed 7 experiments Detail

Instrument

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NMR combined restraints 4 contents Detail