BMRBj - BMREntryMaster

Found 1 Document (0.397 seconds)

BMRB: 30417

6CJD

NMR Structure of Salmonella Type III Secretion system protein OrgC

Authors

Dey, S., De Guzman, R.N.

Assembly

Putative cytoplasmic protein

Entity

1. Putative cytoplasmic protein (polymer, Thiol state: not present), 131 monomers, 14285.82 Da Detail

GHMVSLSARA AMLNNMDSAP LSNGGDVDLY DAFYQRLLAL PESASSETLK DSIYQEMNAF KDPNSGDSAF VSFEQQTAML QNMLAKVEPG THLYEALNGV LVGSMNAQSQ MTSWMQEIIL SGGENKEAID W

Formula weight

14285.82 Da

Source organism

Salmonella enterica subsp. enterica

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.7 %, Completeness: 44.0 %, Completeness (bb): 76.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	44.0 % (644 of 1463)	35.5 % (268 of 754)	44.6 % (251 of 563)	85.6 % (125 of 146)
Backbone	76.1 % (592 of 778)	84.6 % (226 of 267)	63.3 % (243 of 384)	96.9 % (123 of 127)
Sidechain	20.7 % (167 of 807)	8.6 % (42 of 487)	40.9 % (123 of 301)	10.5 % (2 of 19)
Aromatic	5.8 % (6 of 104)	7.7 % (4 of 52)	4.0 % (2 of 50)	0.0 % (0 of 2)
Methyl	14.4 % (19 of 132)	4.5 % (3 of 66)	24.2 % (16 of 66)

1. entity 1

GHMVSLSARA AMLNNMDSAP LSNGGDVDLY DAFYQRLLAL PESASSETLK DSIYQEMNAF KDPNSGDSAF VSFEQQTAML QNMLAKVEPG THLYEALNGV LVGSMNAQSQ MTSWMQEIIL SGGENKEAID W

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 mbar, Temperature 298 K, pH 6.5, Details 1.2 mM [U-99% 15N] OrgC, 1.2 mM [U-13C; U-15N] OrgC, 1.2 mM [U-13C] OrgC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OrgC	[U-99% 15N]	1.2 mM
2	OrgC	[U-13C; U-15N]	1.2 mM
3	OrgC	[U-13C]	1.2 mM
4	MES	natural abundance	2 mM
5	NaCl	natural abundance	75 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: -0.05 ppm, Outliers: 3 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: -0.05 ppm, Outliers: 3 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: 0.15 ppm, Outliers: 2 Detail

Release date

2018-04-08

Citation

A protein secreted by the Salmonella type III secretion system controls needle filament assembly
Kato, J., Dey, S., Soto, J.E., Butan, C., Wilkinson, M.C., De Guzman, R.N., Galan, J.E.
Elife (2018), 7, e35886-e35886, PubMed 30015613 , DOI 10.7554/eLife.35886 , Abstract

Related entities 1. Putative cytoplasmic protein, : 1 entities Detail

Experiments performed 2 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30417_6cjd.nef
Input source #2: Coordindates	6cjd.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

20-------30--------40--------50--------60--------70--------80--------90-------100-------110-------12
GHMVSLSARAAMLNNMDSAPLSNGGDVDLYDAFYQRLLALPESASSETLKDSIYQEMNAFKDPNSGDSAFVSFEQQTAMLQNMLAKVEPGTHLYEALNGV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHMVSLSARAAMLNNMDSAPLSNGGDVDLYDAFYQRLLALPESASSETLKDSIYQEMNAFKDPNSGDSAFVSFEQQTAMLQNMLAKVEPGTHLYEALNGV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------130-------140-------150
LVGSMNAQSQMTSWMQEIILSGGENKEAIDW
|||||||||||||||||||||||||||||||
LVGSMNAQSQMTSWMQEIILSGGENKEAIDW
-------110-------120-------130-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	131	0	0	100.0

Content subtype: combined_30417_6cjd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	604		97.7 (chain: A, length: 131)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1825 (1)	noe	82.4 (chain: A, length: 131)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	70 (1)	hbond	38.2 (chain: A, length: 131)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	104 (104)	.	47.3 (chain: A, length: 131)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 131, Sequence coverage: 97.7%
- Total number of assignments
  - ¹H chemical shifts: 243
  - ¹³C chemical shifts: 238
  - ¹⁵N chemical shifts: 123
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	754	243	32.2
¹³C chemical shifts	563	238	42.3
¹⁵N chemical shifts	148	123	83.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	267	226	84.6
¹³C chemical shifts	262	123	46.9
¹⁵N chemical shifts	127	123	96.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	487	17	3.5
¹³C chemical shifts	301	115	38.2
¹⁵N chemical shifts	21	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	75	1	1.3
¹³C chemical shifts	75	14	18.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	0	0.0
¹³C chemical shifts	50	0	0.0
¹⁵N chemical shifts	2	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 131, Sequence coverage: 82.4%
- Total number of restraints: 1814
- Weight of restraints: 1.0 (1814)
- Potential type of restraints: upper-bound-parabolic (1814)
- Range of distance target values: 2.7, 5.7 (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
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 131, Sequence coverage: 38.2%
  - Total number of restraints: 70
  - Weight of restraints: 1.0 (70)
  - Potential type of restraints: upper-bound-parabolic (70)
  - Range of distance target values: 1.8, 2.7 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 131, Sequence coverage: 47.3%
- Total number of restraints: 104
- Total number of restraints per polymer type: 104
- Weight of restraints: 1.0 (104)
- Potential type of restraints: square-well-parabolic (104)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords PROTEIN BINDING, controls needle assembly of T3SS, early substrate of T3SS

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 (0.397 seconds)

BMRB: 30417

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Putative cytoplasmic protein, : 1 entities Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail