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BMRB: 18181

2LNV

Solution structure of GspC-HR of typeII secretion system

Authors

Gu, S., Kelly, G., Pickersgill, R.

Assembly

GspC-HR of typeII secretion system

Entity

1. GspC-HR of typeII secretion system (polymer, Thiol state: not present), 104 monomers, 11129.22 Da Detail

GSHMLEMAGA LDASQMSNLP PSTLNLSLTG VMAGDDDSRS IAIISKDNEQ FSRGVNEEVP GYNAKIVSIR PDRVVLQYQG RYEVLGLYSQ EDSGSDGVPG AQVR

Formula weight

11129.22 Da

Source organism

Dickeya dadantii

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 70.2 %, Completeness: 66.9 %, Completeness (bb): 67.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	66.9 % (757 of 1131)	68.8 % (404 of 587)	63.8 % (277 of 434)	69.1 % (76 of 110)
Backbone	67.8 % (416 of 614)	68.2 % (146 of 214)	67.1 % (202 of 301)	68.7 % (68 of 99)
Sidechain	66.6 % (406 of 610)	69.2 % (258 of 373)	61.9 % (140 of 226)	72.7 % (8 of 11)
Aromatic	26.1 % (12 of 46)	52.2 % (12 of 23)	0.0 % (0 of 23)
Methyl	69.1 % (76 of 110)	69.1 % (38 of 55)	69.1 % (38 of 55)

1. entity

GSHMLEMAGA LDASQMSNLP PSTLNLSLTG VMAGDDDSRS IAIISKDNEQ FSRGVNEEVP GYNAKIVSIR PDRVVLQYQG RYEVLGLYSQ EDSGSDGVPG AQVR

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 0.5mM 15N 13C OutC-HRF3 20mM Tis pH7.0

#	Name	Isotope labeling	Type	Concentration
1	OutC-HRF3	[U-100% 13C; U-100% 15N]		0.5 mM
2	Tis	natural abundance		20 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

LACS Plot; CA

Referencing offset: 0.19 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.19 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.07 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 0.84 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2LNV, Strand ID: A Detail

Release date

2012-03-08

Citation

Solution structure of homology region (HR) domain of type II secretion system
Gu, S., Kelly, G., Wang, X., Frenkiel, T., Shevchik, V.E., Pickersgill, R.W.
J. Biol. Chem. (2012), 287, 9072-9080, PubMed 22253442 , DOI 10.1074/jbc.M111.300624 , Abstract

Related entities 1. GspC-HR of typeII secretion system, : 1 : 1 : 6 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz MRC NMR centre UK

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 0.5mM 15N 13C OutC-HRF3 20mM Tis pH7.0

#	Name	Isotope labeling	Type	Concentration
1	OutC-HRF3	[U-100% 13C; U-100% 15N]		0.5 mM
2	Tis	natural abundance		20 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

2 3D HNCACB

Instrument

Bruker Avance - 700 MHz MRC NMR centre UK

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 0.5mM 15N 13C OutC-HRF3 20mM Tis pH7.0

#	Name	Isotope labeling	Type	Concentration
1	OutC-HRF3	[U-100% 13C; U-100% 15N]		0.5 mM
2	Tis	natural abundance		20 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz MRC NMR centre UK

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 0.5mM 15N 13C OutC-HRF3 20mM Tis pH7.0

#	Name	Isotope labeling	Type	Concentration
1	OutC-HRF3	[U-100% 13C; U-100% 15N]		0.5 mM
2	Tis	natural abundance		20 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

4 3D 1H-15N TOCSY

Instrument

Bruker Avance - 700 MHz MRC NMR centre UK

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 0.5mM 15N 13C OutC-HRF3 20mM Tis pH7.0

#	Name	Isotope labeling	Type	Concentration
1	OutC-HRF3	[U-100% 13C; U-100% 15N]		0.5 mM
2	Tis	natural abundance		20 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz MRC NMR centre UK

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 0.5mM 15N 13C OutC-HRF3 20mM Tis pH7.0

#	Name	Isotope labeling	Type	Concentration
1	OutC-HRF3	[U-100% 13C; U-100% 15N]		0.5 mM
2	Tis	natural abundance		20 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

6 3D HNHA

Instrument

Bruker Avance - 700 MHz MRC NMR centre UK

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 0.5mM 15N 13C OutC-HRF3 20mM Tis pH7.0

#	Name	Isotope labeling	Type	Concentration
1	OutC-HRF3	[U-100% 13C; U-100% 15N]		0.5 mM
2	Tis	natural abundance		20 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

7 3D HNCO

Instrument

Bruker Avance - 700 MHz MRC NMR centre UK

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 0.5mM 15N 13C OutC-HRF3 20mM Tis pH7.0

#	Name	Isotope labeling	Type	Concentration
1	OutC-HRF3	[U-100% 13C; U-100% 15N]		0.5 mM
2	Tis	natural abundance		20 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz MRC NMR centre UK

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 0.5mM 15N 13C OutC-HRF3 20mM Tis pH7.0

#	Name	Isotope labeling	Type	Concentration
1	OutC-HRF3	[U-100% 13C; U-100% 15N]		0.5 mM
2	Tis	natural abundance		20 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

9 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz MRC NMR centre UK

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 0.5mM 15N 13C OutC-HRF3 20mM Tis pH7.0

#	Name	Isotope labeling	Type	Concentration
1	OutC-HRF3	[U-100% 13C; U-100% 15N]		0.5 mM
2	Tis	natural abundance		20 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz MRC NMR centre UK

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 0.5mM 15N 13C OutC-HRF3 20mM Tis pH7.0

#	Name	Isotope labeling	Type	Concentration
1	OutC-HRF3	[U-100% 13C; U-100% 15N]		0.5 mM
2	Tis	natural abundance		20 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

11 3D HNCA

Instrument

Bruker Avance - 700 MHz MRC NMR centre UK

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 0.5mM 15N 13C OutC-HRF3 20mM Tis pH7.0

#	Name	Isotope labeling	Type	Concentration
1	OutC-HRF3	[U-100% 13C; U-100% 15N]		0.5 mM
2	Tis	natural abundance		20 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

12 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz MRC NMR centre UK

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 0.5mM 15N 13C OutC-HRF3 20mM Tis pH7.0

#	Name	Isotope labeling	Type	Concentration
1	OutC-HRF3	[U-100% 13C; U-100% 15N]		0.5 mM
2	Tis	natural abundance		20 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, RDC restraints	combined_18181_2lnv.nef
Input source #2: Coordindates	2lnv.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

70-------80--------90-------100-------110-------120-------130-------140-------150-------160-------17
GSHMLEMAGALDASQMSNLPPSTLNLSLTGVMAGDDDSRSIAIISKDNEQFSRGVNEEVPGYNAKIVSIRPDRVVLQYQGRYEVLGLYSQEDSGSDGVPG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMLEMAGALDASQMSNLPPSTLNLSLTGVMAGDDDSRSIAIISKDNEQFSRGVNEEVPGYNAKIVSIRPDRVVLQYQGRYEVLGLYSQEDSGSDGVPG
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0---
AQVR
||||
AQVR
----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	104	0	0	100.0

Content subtype: combined_18181_2lnv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	696		63.5 (chain: A, length: 104)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	28 (1)	hbond	23.1 (chain: A, length: 104)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	58 (58)	.	55.8 (chain: A, length: 104)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 63.5%
- Total number of assignments
  - ¹H chemical shifts: 364
  - ¹³C chemical shifts: 260
  - ¹⁵N chemical shifts: 72
- 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_4
- Status: Warning
- Experiment type: hbond
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 23.1%
- Total number of restraints: 28
- Weight of restraints: 1.0 (28)
- Potential type of restraints: square-well-parabolic (28)
- Range of distance target values: 2.1, 3.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 55.8%

70-------80--------90-------100-------110-------120-------130-------140-------150-------160-------17
GSHMLEMAGALDASQMSNLPPSTLNLSLTGVMAGDDDSRSIAIISKDNEQFSRGVNEEVPGYNAKIVSIRPDRVVLQYQGRYEVLGLYSQEDSGSDGVPG
           |||||     |   |||||||| || ||  |||||||||| ||||||  |||| |  || | |||||||||||||||  |         
...........DASQM.....S...LSLTGVMA.DD.SR..AIISKDNEQF.RGVNEE..GYNA.I..IR.D.VVLQYQGRYEVLGLY..E         
70-------80--------90-------100-------110-------120-------130-------140-------150-------160         

0---
AQVR

Total number of restraints: 58
Potential type of restraints: undefined (58)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords GspC, OutC