BMRBj - BMREntryMaster

Found 1 Document (0.759 seconds)

BMRB: 34376

6R0J

The N-terminal domain of rhomboid protease YqgP

Authors

Began, J., Strisovsky, K., Veverka, V.

Assembly

Rhomboid family serine protease

Entity

1. Rhomboid family serine protease (polymer), 185 monomers, 21805.29 Da Detail

MFLLEYTYWK IAAHLVNSGY GVIQAGESDE IWLEAPDKSS HDLVRLYKHD LDFRQEMVRD IEEQAERVER VRHQLGRRRM KLLNVFFSTE APVDDWEEIA KKTFEKGTVS VEPAIVRGTM LRDDLQAVFP SFRTEDCSEE HASFENAQMA RERFLSLVLK QEEQRKTEAA VFQNGKLERE NLYFQ

Formula weight

21805.29 Da

Source organism

Bacillus subtilis

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.5 %, Completeness: 92.6 %, Completeness (bb): 98.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.6 % (2069 of 2235)	93.5 % (1094 of 1170)	90.5 % (784 of 866)	96.0 % (191 of 199)
Backbone	98.6 % (1087 of 1102)	98.4 % (367 of 373)	99.3 % (544 of 548)	97.2 % (176 of 181)
Sidechain	88.4 % (1159 of 1311)	91.2 % (727 of 797)	84.1 % (417 of 496)	83.3 % (15 of 18)
Aromatic	72.3 % (149 of 206)	87.4 % (90 of 103)	56.0 % (56 of 100)	100.0 % (3 of 3)
Methyl	99.5 % (189 of 190)	100.0 % (95 of 95)	98.9 % (94 of 95)

1. entity 1

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM [U-13C; U-15N] YqgP, 150 mM sodium chloride, 25 mM sodium phosphate, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	YqgP	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.24 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.24 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.16 ppm, Outliers: 5 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.07 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 30 models in PDB: 6R0J, Strand ID: A Detail

Release date

2020-01-01

Citation

Rhomboid intramembrane protease YqgP licenses bacterial membrane protein quality control as adaptor of FtsH AAA protease
Began, J., Cordier, B., Brezinova, J., Delisle, J., Hexnerova, R., Srb, P., Rampirova, P., Kozisek, M., Baudet, M., Coute, Y., Galinier, A., Veverka, V., Doan, T., Strisovsky, K.
EMBO J. (2020), 39, e102935-e102935, PubMed 31930742 , DOI 10.15252/embj.2019102935 , Abstract

Related entities 1. Rhomboid family serine protease, : 1 : 1 entities Detail

Experiments performed 6 experiments Detail

1 3D HNCACB

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM [U-13C; U-15N] YqgP, 150 mM sodium chloride, 25 mM sodium phosphate, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	YqgP	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM

2 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	YqgP	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM

3 3D HNCO

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	YqgP	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM

4 3D HCCH-TOCSY

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	YqgP	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM

5 3D 1H-15N NOESY

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	YqgP	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM

6 3D 1H-13C NOESY

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	YqgP	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34376_3.str
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

Content subtype: bmr34376_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	2244		99.5 (chain: 1, length: 185)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 185, Sequence coverage: 99.5%
- Total number of assignments
  - ¹H chemical shifts: 1279
  - ¹³C chemical shifts: 773
  - ¹⁵N chemical shifts: 192
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1170	1081	92.4
¹³C chemical shifts	866	773	89.3
¹⁵N chemical shifts	215	192	89.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	373	367	98.4
¹³C chemical shifts	370	367	99.2
¹⁵N chemical shifts	181	176	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	797	714	89.6
¹³C chemical shifts	496	406	81.9
¹⁵N chemical shifts	34	16	47.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	100	99	99.0
¹³C chemical shifts	100	98	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	103	90	87.4
¹³C chemical shifts	100	54	54.0
¹⁵N chemical shifts	3	3	100.0

Keywords Bacillus subtilis, MEMBRANE PROTEIN, metal binding, rhomboid protease

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Found 1 Document (0.759 seconds)

BMRB: 34376

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Rhomboid family serine protease, : 1 : 1 entities Detail

Experiments performed 6 experiments Detail

Instrument

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Chemical shift validation 3 contents Detail