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BMRB: 27085

6QBZ

1H, 13C, 15N backbone NMR assignment of N-terminal domain of SaHPF

Authors

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

Assembly

HPF

Entity

1. HPF (polymer, Thiol state: not present), 110 monomers, 12907.53 Da Detail

MIRFEIHGDN LTITDAIRNY IEEKIGKLER YFNDVPNAVA HVKVKTYSNS ATKIEVTIPL KNVTLRAEER NDDLYAGIDL INNKLERQVR KYKTRINRKS RDRGDQEVFV

Formula weight

12907.53 Da

Source organism

Staphylococcus aureus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 98.2 %, Completeness: 74.8 %, Completeness (bb): 96.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.8 % (999 of 1335)	64.4 % (452 of 702)	86.2 % (442 of 513)	87.5 % (105 of 120)
Backbone	96.6 % (634 of 656)	95.5 % (212 of 222)	98.2 % (320 of 326)	94.4 % (102 of 108)
Sidechain	59.7 % (469 of 785)	50.0 % (240 of 480)	77.1 % (226 of 293)	25.0 % (3 of 12)
Aromatic	14.1 % (11 of 78)	17.9 % (7 of 39)	10.3 % (4 of 39)
Methyl	70.9 % (95 of 134)	61.2 % (41 of 67)	80.6 % (54 of 67)

1. SaHPF NTD

MIRFEIHGDN LTITDAIRNY IEEKIGKLER YFNDVPNAVA HVKVKTYSNS ATKIEVTIPL KNVTLRAEER NDDLYAGIDL INNKLERQVR KYKTRINRKS RDRGDQEVFV

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 308.000 K, pH 7.600

#	Name	Isotope labeling	Type	Concentration
1	SaHPF NTD	[U-100% 13C; U-100% 15N]		0.62 mM
2	NH4Cl	natural abundance		200.00 mM

LACS Plot; CA

Referencing offset: -1.09 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -1.09 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.35 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 6QBZ, Strand ID: A Detail

Release date

2017-04-26

Citation

NMR assignments of the N-terminal domain of Staphylococcus aureus hibernation promoting factor (SaHPF)
Usachev, K., Ayupov, R., Validov, S., Khusainov, I., Yusupov, M.
Biomol. NMR Assign. (2017), 12, 85-89, PubMed 28980143 , DOI 10.1007/s12104-017-9783-2 , Abstract

Related entities 1. HPF, : 1 : 7 : 2 : 84 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC/HMQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 308.000 K, pH 7.600

#	Name	Isotope labeling	Type	Concentration
1	SaHPF NTD	[U-100% 13C; U-100% 15N]		0.62 mM
2	NH4Cl	natural abundance		200.00 mM

2 2D 1H-13C HSQC/HMQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 308.000 K, pH 7.600

#	Name	Isotope labeling	Type	Concentration
1	SaHPF NTD	[U-100% 13C; U-100% 15N]		0.62 mM
2	NH4Cl	natural abundance		200.00 mM

3 2D 1H-13C HSQC/HMQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 308.000 K, pH 7.600

#	Name	Isotope labeling	Type	Concentration
1	SaHPF NTD	[U-100% 13C; U-100% 15N]		0.62 mM
2	NH4Cl	natural abundance		200.00 mM

4 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 308.000 K, pH 7.600

#	Name	Isotope labeling	Type	Concentration
1	SaHPF NTD	[U-100% 13C; U-100% 15N]		0.62 mM
2	NH4Cl	natural abundance		200.00 mM

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 308.000 K, pH 7.600

#	Name	Isotope labeling	Type	Concentration
1	SaHPF NTD	[U-100% 13C; U-100% 15N]		0.62 mM
2	NH4Cl	natural abundance		200.00 mM

6 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 308.000 K, pH 7.600

#	Name	Isotope labeling	Type	Concentration
1	SaHPF NTD	[U-100% 13C; U-100% 15N]		0.62 mM
2	NH4Cl	natural abundance		200.00 mM

7 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 308.000 K, pH 7.600

#	Name	Isotope labeling	Type	Concentration
1	SaHPF NTD	[U-100% 13C; U-100% 15N]		0.62 mM
2	NH4Cl	natural abundance		200.00 mM

8 HN(CA)CO (H[N[ca[CO]]])

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 308.000 K, pH 7.600

#	Name	Isotope labeling	Type	Concentration
1	SaHPF NTD	[U-100% 13C; U-100% 15N]		0.62 mM
2	NH4Cl	natural abundance		200.00 mM

9 CC(CO)NH (C_coNH.relayed)

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 308.000 K, pH 7.600

#	Name	Isotope labeling	Type	Concentration
1	SaHPF NTD	[U-100% 13C; U-100% 15N]		0.62 mM
2	NH4Cl	natural abundance		200.00 mM

10 3D H(CCO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 308.000 K, pH 7.600

#	Name	Isotope labeling	Type	Concentration
1	SaHPF NTD	[U-100% 13C; U-100% 15N]		0.62 mM
2	NH4Cl	natural abundance		200.00 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_27085_6qbz.nef
Input source #2: Coordindates	6qbz.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
MIRFEIHGDNLTITDAIRNYIEEKIGKLERYFNDVPNAVAHVKVKTYSNSATKIEVTIPLKNVTLRAEERNDDLYAGIDLINNKLERQVRKYKTRINRKS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MIRFEIHGDNLTITDAIRNYIEEKIGKLERYFNDVPNAVAHVKVKTYSNSATKIEVTIPLKNVTLRAEERNDDLYAGIDLINNKLERQVRKYKTRINRKS

-------110
RDRGDQEVFV
||||||||||
RDRGDQEVFV

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	110	0	0	100.0

Content subtype: combined_27085_6qbz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	964		98.2 (chain: A, length: 110)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	1724 (1)	noe	98.2 (chain: A, length: 110)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 98.2%
- Total number of assignments
  - ¹H chemical shifts: 427
  - ¹³C chemical shifts: 435
  - ¹⁵N chemical shifts: 102
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 98.2%
- Total number of restraints: 1724
- Weight of restraints: 1.0 (1724)
- Potential type of restraints: square-well-parabolic (1724)
- Range of distance target values: 2.2, 4.5 (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

Keywords HPF, Hibernation, Pathogen, Ribosome, Staphylococcus aureus, hibernation, ribosome