BMRBj - BMREntryMaster

Found 1 Document (1.138 seconds)

BMRB: 34424

6SJX

Precursor structure of the self-processing module of iron-regulated FrpC of N. Meningitidis with calcium ions

Authors

Kuban, V., Macek, P., Hritz, J., Nechvatalova, K., Nedbalcova, K., Faldyna, M., Zidek, L., Bumba, L.

Assembly

Iron-regulated protein FrpA

Entity

1. Iron-regulated protein FrpA, entity 1 (polymer, Thiol state: not present), 182 monomers, 19230.73 Da Detail

GSDALALDLD GDGIETVATK GFSGSLFDHN RDGIRTATGW VSADDGLLVR DLNGNGIIDN GAELFGDNTK LADGSFAKHG YAALAELDSN GDNIINAADA AFQSLRVWQD LNQDGISQAN ELRTLEELGI QSLDLAYKDV NKNLGNGNTL AQQGSYTKTN GTTAKMGDLL LAADNLHSRF LE

2. Iron-regulated protein FrpA, entity CA (non-polymer), 40.078 × 5 Da

Total weight

19431.121 Da

Max. entity weight

19230.73 Da

Source organism

Neisseria meningitidis serogroup C

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 85.2 %, Completeness: 78.4 %, Completeness (bb): 83.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.4 % (1533 of 1956)	77.6 % (774 of 998)	79.2 % (595 of 751)	79.2 % (164 of 207)
Backbone	83.0 % (906 of 1092)	81.9 % (316 of 386)	83.8 % (439 of 524)	83.0 % (151 of 182)
Sidechain	74.7 % (765 of 1024)	74.8 % (458 of 612)	76.0 % (294 of 387)	52.0 % (13 of 25)
Aromatic	30.8 % (37 of 120)	31.7 % (19 of 60)	29.3 % (17 of 58)	50.0 % (1 of 2)
Methyl	88.9 % (192 of 216)	88.9 % (96 of 108)	88.9 % (96 of 108)

1. entity 1

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 7.4, Details 5 mM TRIS, 50 mM sodium chloride, 0.1 % sodium azide, 10 mM Calcium chloride, 0.35 mM [U-99% 13C; U-99% 15N] P415A mutant of Self-processing module of FrpC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	5 mM
2	sodium chloride	natural abundance	50 mM
3	sodium azide	natural abundance	0.1 %
4	Calcium chloride	natural abundance	10 mM
5	P415A mutant of Self-processing module of FrpC	[U-99% 13C; U-99% 15N]	0.35 (±0.05) mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 7.4, Details 50 mM TRIS, 50 mM sodium chloride, 0.1 % sodium azide, 0.707 mM P415A mutant of Self-processing module of FrpC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	TRIS	natural abundance	50 mM
7	sodium chloride	natural abundance	50 mM
8	sodium azide	natural abundance	0.1 %
9	P415A mutant of Self-processing module of FrpC	natural abundance	0.707 (±0.005) mM

Protein Blocks Logo

Calculated from 14 models in PDB: 6SJX, Strand ID: A Detail

Release date

2019-08-15

Citation

Structural Basis of Ca²⁺-Dependent Self-Processing Activity of Repeat-in-Toxin Proteins
Kuban, V., Macek, P., Hritz, J., Nechvatalova, K., Nedbalcova, K., Faldyna, M., Zidek, L., Bumba, L.
mBio (2020), 11, e00226-20-e00226-20, PubMed 32184239 , DOI 10.1128/mBio.00226-20 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 28058 released on 2020-01-02
Title NMR assignment of self-processing module of FrpC protein of Neisseria meningitidis loaded with calcium ions

Related entities 1. Iron-regulated protein FrpA, entity 1, : 1 : 1 : 5 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 7.4, Details 5 mM TRIS, 50 mM sodium chloride, 0.1 % sodium azide, 10 mM Calcium chloride, 0.35 mM [U-99% 13C; U-99% 15N] P415A mutant of Self-processing module of FrpC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	5 mM
2	sodium chloride	natural abundance	50 mM
3	sodium azide	natural abundance	0.1 %
4	Calcium chloride	natural abundance	10 mM
5	P415A mutant of Self-processing module of FrpC	[U-99% 13C; U-99% 15N]	0.35 (±0.05) mM

2 3D HNCO

Instrument

Bruker AVANCE III - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	5 mM
2	sodium chloride	natural abundance	50 mM
3	sodium azide	natural abundance	0.1 %
4	Calcium chloride	natural abundance	10 mM
5	P415A mutant of Self-processing module of FrpC	[U-99% 13C; U-99% 15N]	0.35 (±0.05) mM

3 3D HNCACB

Instrument

Bruker AVANCE III - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	5 mM
2	sodium chloride	natural abundance	50 mM
3	sodium azide	natural abundance	0.1 %
4	Calcium chloride	natural abundance	10 mM
5	P415A mutant of Self-processing module of FrpC	[U-99% 13C; U-99% 15N]	0.35 (±0.05) mM

4 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	5 mM
2	sodium chloride	natural abundance	50 mM
3	sodium azide	natural abundance	0.1 %
4	Calcium chloride	natural abundance	10 mM
5	P415A mutant of Self-processing module of FrpC	[U-99% 13C; U-99% 15N]	0.35 (±0.05) mM

5 3D HCCH-TOCSY

Instrument

Bruker AVANCE III - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	5 mM
2	sodium chloride	natural abundance	50 mM
3	sodium azide	natural abundance	0.1 %
4	Calcium chloride	natural abundance	10 mM
5	P415A mutant of Self-processing module of FrpC	[U-99% 13C; U-99% 15N]	0.35 (±0.05) mM

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE III - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	5 mM
2	sodium chloride	natural abundance	50 mM
3	sodium azide	natural abundance	0.1 %
4	Calcium chloride	natural abundance	10 mM
5	P415A mutant of Self-processing module of FrpC	[U-99% 13C; U-99% 15N]	0.35 (±0.05) mM

7 3D 1H-15N NOESY

Instrument

Bruker AVANCE III - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	TRIS	natural abundance	5 mM
2	sodium chloride	natural abundance	50 mM
3	sodium azide	natural abundance	0.1 %
4	Calcium chloride	natural abundance	10 mM
5	P415A mutant of Self-processing module of FrpC	[U-99% 13C; U-99% 15N]	0.35 (±0.05) mM

8 1D WATERGATE W5

Instrument

Bruker AVANCE III - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 7.4, Details 50 mM TRIS, 50 mM sodium chloride, 0.1 % sodium azide, 0.707 mM P415A mutant of Self-processing module of FrpC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	TRIS	natural abundance	50 mM
7	sodium chloride	natural abundance	50 mM
8	sodium azide	natural abundance	0.1 %
9	P415A mutant of Self-processing module of FrpC	natural abundance	0.707 (±0.005) mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34424_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: bmr34424_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1665		81.9 (chain: 1, length: 182)
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: 182, Sequence coverage: 81.9%
- Total number of assignments
  - ¹H chemical shifts: 933
  - ¹³C chemical shifts: 576
  - ¹⁵N chemical shifts: 156
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
93	ASN	CG	178.381
103	GLN	CD	180.239
131	GLN	CD	179.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	998	739	74.0
¹³C chemical shifts	751	573	76.3
¹⁵N chemical shifts	213	156	73.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	386	303	78.5
¹³C chemical shifts	364	288	79.1
¹⁵N chemical shifts	182	144	79.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	612	436	71.2
¹³C chemical shifts	387	285	73.6
¹⁵N chemical shifts	31	12	38.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	109	97	89.0
¹³C chemical shifts	109	97	89.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	16	26.7
¹³C chemical shifts	58	14	24.1
¹⁵N chemical shifts	2	1	50.0

Keywords METAL BINDING PROTEIN, Repeat in toxin proteins, calcium

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (1.138 seconds)

BMRB: 34424

Sample #1

Sample #2

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Iron-regulated protein FrpA, entity 1, : 1 : 1 : 5 entities Detail

Experiments performed 8 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 4 contents Detail