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Found 1 Document (0.724 seconds)

BMRB: 34120

5NKO

Solution structure of the C-terminal domain of S. aureus Hibernating Promoting Factor (CTD-SaHPF)

Authors

Usachev, K.S., Khusainov, I.S., Ayupov, R.K., Validov, S.Z., Kieffer, B., Yusupov, M.M.

Assembly

Ribosome hibernation promotion factor

Entity

1. Ribosome hibernation promotion factor (polymer, Thiol state: not present), 61 monomers, 7114.996 × 2 Da Detail

MIEIIRSKEF SLKPMDSEEA VLQMNLLGHD FFVFTDRETD GTSIVYRRKD GKYGLIQTSE Q

Total weight

14229.992 Da

Max. entity weight

7114.996 Da

Source organism

Staphylococcus aureus subsp. aureus NCTC 8325

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 86.4 %, Completeness (bb): 95.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.4 % (634 of 734)	82.0 % (315 of 384)	90.6 % (259 of 286)	93.8 % (60 of 64)
Backbone	95.3 % (347 of 364)	93.6 % (117 of 125)	97.2 % (174 of 179)	93.3 % (56 of 60)
Sidechain	80.3 % (343 of 427)	76.4 % (198 of 259)	86.0 % (141 of 164)	100.0 % (4 of 4)
Aromatic	58.3 % (35 of 60)	60.0 % (18 of 30)	56.7 % (17 of 30)
Methyl	98.4 % (61 of 62)	96.8 % (30 of 31)	100.0 % (31 of 31)

1. entity 1

MIEIIRSKEF SLKPMDSEEA VLQMNLLGHD FFVFTDRETD GTSIVYRRKD GKYGLIQTSE Q

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 308 K, pH 7.6, Details 2.0 mM [U-99% 13C; U-99% 15N] C-terminal domain of SaHPF, 50 mM potassium phosphate, 250 mM NH4Cl, 90% H2O/10% D2O.

#	Name	Isotope labeling	Concentration
1	C-terminal domain of SaHPF	[U-99% 13C; U-99% 15N]	2.0 mM
2	NH4Cl	natural abundance	250 mM
3	potassium phosphate	natural abundance	50 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0

Referencing offset: -0.07 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0

Referencing offset: -0.07 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0

Referencing offset: 0.16 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 5NKO, Strand ID: A, B Detail

Release date

2017-04-02

Citation

Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF
Khusainov, I., Vicens, Q., Ayupov, R., Usachev, K., Myasnikov, A., Simonetti, A., Validov, S., Kieffer, B., Yusupova, G., Yusupov, M., Hashem, Y.
EMBO J. (2017), 36, 2073-2087, PubMed 28645916 , DOI 10.15252/embj.201696105 , Abstract

Entries sharing articles EMDB: 4 entries Detail

  EMDB: 3624 released on 2017-04-05
    Title Hibernating ribosome from Staphylococcus aureus (Unrotated state)
  EMDB: 3625 released on 2017-04-05
    Title Hibernating ribosome from Staphylococcus aureus (Rotated state)
  EMDB: 3638 released on 2017-03-29
    Title 100S disome from Staphylococcus aureus (Tight conformation)
  EMDB: 3639 released on 2017-03-29
    Title 100S disome from Staphylococcus aureus (Loose conformation)

Related entities 1. Ribosome hibernation promotion factor, : 1 : 1 : 9 : 37 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34120_5nko.nef
Input source #2: Coordindates	5nko.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

130-----140-------150-------160-------170-------180-------190
MIEIIRSKEFSLKPMDSEEAVLQMNLLGHDFFVFTDRETDGTSIVYRRKDGKYGLIQTSEQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MIEIIRSKEFSLKPMDSEEAVLQMNLLGHDFFVFTDRETDGTSIVYRRKDGKYGLIQTSEQ
--------10--------20--------30--------40--------50--------60-

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

130-----140-------150-------160-------170-------180-------190
MIEIIRSKEFSLKPMDSEEAVLQMNLLGHDFFVFTDRETDGTSIVYRRKDGKYGLIQTSEQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MIEIIRSKEFSLKPMDSEEAVLQMNLLGHDFFVFTDRETDGTSIVYRRKDGKYGLIQTSEQ
--------10--------20--------30--------40--------50--------60-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	61	0	0	100.0
B	B	61	0	0	100.0

Content subtype: combined_34120_5nko.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1276		98.4 (chain: A, length: 61), 98.4 (chain: B, length: 61)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	2242 (1)	noe	98.4 (chain: A, length: 61), 98.4 (chain: B, length: 61)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	108 (1)	hbond	55.7 (chain: A, length: 61), 55.7 (chain: B, length: 61)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	228 (228)	.	96.7 (chain: A, length: 61), 96.7 (chain: B, length: 61)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 98.4%
  - Entity_assembly_ID: B, Chain length: 61, Sequence coverage: 98.4%
- Total number of assignments
  - ¹H chemical shifts: 640
  - ¹³C chemical shifts: 516
  - ¹⁵N chemical shifts: 120
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	384	320	83.3
¹³C chemical shifts	286	258	90.2
¹⁵N chemical shifts	68	60	88.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	125	119	95.2
¹³C chemical shifts	122	118	96.7
¹⁵N chemical shifts	60	56	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	259	201	77.6
¹³C chemical shifts	164	140	85.4
¹⁵N chemical shifts	8	4	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	30	88.2
¹³C chemical shifts	34	31	91.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	20	66.7
¹³C chemical shifts	30	17	56.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	384	320	83.3
¹³C chemical shifts	286	258	90.2
¹⁵N chemical shifts	68	60	88.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	125	119	95.2
¹³C chemical shifts	122	118	96.7
¹⁵N chemical shifts	60	56	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	259	201	77.6
¹³C chemical shifts	164	140	85.4
¹⁵N chemical shifts	8	4	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	30	88.2
¹³C chemical shifts	34	31	91.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	20	66.7
¹³C chemical shifts	30	17	56.7

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 98.4%
  - Entity_assembly_ID: B, Chain length: 61, Sequence coverage: 98.4%
- Total number of restraints: 2242
- Weight of restraints: 1.0 (2242)
- Potential type of restraints: square-well-parabolic (2242)
- Range of distance target values: 2.2, 6.75 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- 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: 61, Sequence coverage: 55.7%
    - Entity_assembly_ID: B, Chain length: 61, Sequence coverage: 55.7%
  - Total number of restraints: 108
  - Weight of restraints: 1.0 (108)
  - Potential type of restraints: square-well-parabolic (108)
  - Range of distance target values: 2.21, 3.22 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - 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: 61, Sequence coverage: 96.7%
  - Entity_assembly_ID: B, Chain length: 61, Sequence coverage: 96.7%
- Total number of restraints: 228
- Total number of restraints per polymer type: 228
- Weight of restraints: 1.0 (228)
- Potential type of restraints: square-well-parabolic (228)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords HPF, Hibernating Promoting Factor, Hibernation, Pathogen, Ribosome, Staphylococcus aureus, ribosomal protein

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Found 1 Document (0.724 seconds)

BMRB: 34120

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles EMDB: 4 entries Detail

Related entities 1. Ribosome hibernation promotion factor, : 1 : 1 : 9 : 37 entities Detail

Experiments performed 4 experiments Detail

Instrument

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Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail