BMRBj - BMREntryMaster

Found 1 Document (0.416 seconds)

BMRB: 34666

7PQ4

NMR Structure of RgpB C-terminal Domain

Authors

Dorgan, B.J., Curtis, M.A., Garnett, J.A.

Assembly

Arginine-specific cysteine proteinase (Arg-gingipain)

Entity

1. Arginine-specific cysteine proteinase (Arg-gingipain) (polymer, Thiol state: not present), 90 monomers, 9836.999 Da Detail

MAHHHHHHVD DDDKMGTSIA DVANDKPYTV AVSGKTITVE SPAAGLTIFD MNGRRVATAK NRMVFEAQNG VYAVRIATEG KTYTEKVIVK

Formula weight

9836.999 Da

Source organism

Porphyromonas gingivalis

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.2 %, Completeness: 83.2 %, Completeness (bb): 85.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.2 % (829 of 996)	78.5 % (397 of 506)	89.1 % (350 of 393)	84.5 % (82 of 97)
Backbone	85.6 % (459 of 536)	78.3 % (144 of 184)	89.8 % (237 of 264)	88.6 % (78 of 88)
Sidechain	80.1 % (436 of 544)	76.7 % (247 of 322)	86.9 % (185 of 213)	44.4 % (4 of 9)
Aromatic	60.3 % (41 of 68)	61.8 % (21 of 34)	58.8 % (20 of 34)
Methyl	92.6 % (100 of 108)	87.0 % (47 of 54)	98.1 % (53 of 54)

1. entity 1

MAHHHHHHVD DDDKMGTSIA DVANDKPYTV AVSGKTITVE SPAAGLTIFD MNGRRVATAK NRMVFEAQNG VYAVRIATEG KTYTEKVIVK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6, Details 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RgpB-CTD (G662-K736)	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		2 mM

Release date

2021-10-24

Related entities 1. Arginine-specific cysteine proteinase (Arg-gingipain), : 1 : 2 : 12 entities Detail

Interaction partners 1. Arginine-specific cysteine proteinase (Arg-gingipain), : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6, Details 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RgpB-CTD (G662-K736)	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		2 mM

2 3D HNCO

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6, Details 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RgpB-CTD (G662-K736)	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		2 mM

3 3D HNCACO

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6, Details 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RgpB-CTD (G662-K736)	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		2 mM

4 3D HNCACB

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6, Details 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RgpB-CTD (G662-K736)	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		2 mM

5 3D CBCA(CO)NH

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6, Details 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RgpB-CTD (G662-K736)	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		2 mM

6 3D H(CCO)NH

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6, Details 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RgpB-CTD (G662-K736)	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		2 mM

7 3D C(CO)NH

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6, Details 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RgpB-CTD (G662-K736)	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		2 mM

8 3D HCCH-TOCSY

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6, Details 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RgpB-CTD (G662-K736)	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		2 mM

9 3D CCH-TOCSY

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6, Details 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RgpB-CTD (G662-K736)	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		2 mM

10 HBCBCGCDHD

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6, Details 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RgpB-CTD (G662-K736)	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		2 mM

11 HBCBCGCDCEHE

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6, Details 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RgpB-CTD (G662-K736)	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		2 mM

12 3D 1H-13C NOESY

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6, Details 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RgpB-CTD (G662-K736)	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		2 mM

13 3D 1H-15N NOESY

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6, Details 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RgpB-CTD (G662-K736)	[U-13C; U-15N]		1 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		2 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34666_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	OK

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr34666_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	977		92.2 (chain: 1, length: 90)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 90, Sequence coverage: 92.2%
- Total number of assignments
  - ¹H chemical shifts: 541
  - ¹³C chemical shifts: 353
  - ¹⁵N chemical shifts: 83
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Keywords CTD, Ig-like, PROTEIN TRANSPORT, T9SS, gingipain