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BMRB: 18618

2LWB

Structural model of BAD-1 repeat loop by NMR

Authors

Brandhorst, T., Klein, B., Tonelli, M.

Assembly

BAD-1 repeat loop

Entity

1. BAD-1 repeat loop (polymer), 20 monomers, 2686.884 Da Detail

NCDWDKSHEK YDWELWDKWC

Formula weight

2686.884 Da

Source organism

Blastomyces dermatitidis

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.1 %, Completeness (bb): 83.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.1 % (236 of 262)	98.5 % (135 of 137)	76.0 % (76 of 100)	100.0 % (25 of 25)
Backbone	83.3 % (100 of 120)	100.0 % (40 of 40)	66.7 % (40 of 60)	100.0 % (20 of 20)
Sidechain	96.3 % (156 of 162)	97.9 % (95 of 97)	93.3 % (56 of 60)	100.0 % (5 of 5)
Aromatic	90.0 % (54 of 60)	93.3 % (28 of 30)	84.6 % (22 of 26)	100.0 % (4 of 4)
Methyl	100.0 % (4 of 4)	100.0 % (2 of 2)	100.0 % (2 of 2)

1. BAD-1 repeat loop

NCDWDKSHEK YDWELWDKWC

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	TR4	[U-100% 13C; U-100% 15N]		0.1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 18 models in PDB: 2LWB, Strand ID: A Detail

Release date

2013-07-28

Citation

Structure and function of a fungal adhesin that binds heparin and mimics thrombospondin-1 by blocking T cell activation and effector function
Brandhorst, T., Roy, R., Wuthrich, M., Nanjappa, S., Filutowicz, H., Galles, K., Tonelli, M., McCaslin, D.R., Satyshur, K., Klein, B.
PLoS Pathog. (2013), 9, e1003464-e1003464, PubMed 23853587 , DOI 10.1371/journal.ppat.1003464 , Abstract

Related entities 1. BAD-1 repeat loop, : 1 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian VNMRS - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	TR4	[U-100% 13C; U-100% 15N]		0.1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Varian VNMRS - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	TR4	[U-100% 13C; U-100% 15N]		0.1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Varian VNMRS - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	TR4	[U-100% 13C; U-100% 15N]		0.1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

4 3D CBCA(CO)NH

Instrument

Varian VNMRS - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	TR4	[U-100% 13C; U-100% 15N]		0.1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

5 3D HBHA(CO)NH

Instrument

Varian VNMRS - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	TR4	[U-100% 13C; U-100% 15N]		0.1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

6 3D H(CCO)NH

Instrument

Varian VNMRS - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	TR4	[U-100% 13C; U-100% 15N]		0.1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

7 3D C(CO)NH

Instrument

Varian VNMRS - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	TR4	[U-100% 13C; U-100% 15N]		0.1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

8 3D HCCH-TOCSY

Instrument

Varian VNMRS - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	TR4	[U-100% 13C; U-100% 15N]		0.1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

9 3D 1H-15N NOESY

Instrument

Varian VNMRS - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	TR4	[U-100% 13C; U-100% 15N]		0.1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

10 2D 1H-13C HSQC aliphatic

Instrument

Varian VNMRS - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	TR4	[U-100% 13C; U-100% 15N]		0.1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

11 2D 1H-13C HSQC aromatic

Instrument

Varian VNMRS - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 8.0

#	Name	Isotope labeling	Type	Concentration
1	TR4	[U-100% 13C; U-100% 15N]		0.1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18618_2lwb.nef
Input source #2: Coordindates	2lwb.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:19:CYS:SG	A:37:CYS:SG	oxidized, CA 56.054, CB 37.659 ppm	oxidized, CA 53.694, CB 39.088 ppm	1.886

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-------
NCDWDKSHEKYDWELWDKWC
||||||||||||||||||||
NCDWDKSHEKYDWELWDKWC
--------10--------20

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	20	0	0	100.0

Content subtype: combined_18618_2lwb.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	234		100.0 (chain: A, length: 20)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	608 (1)	noe	100.0 (chain: A, length: 20)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 134
  - ¹³C chemical shifts: 76
  - ¹⁵N chemical shifts: 24
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 100.0%
- Total number of restraints: 608
- Weight of restraints: 1.0 (608)
- Potential type of restraints: upper-bound-parabolic (608)
- Range of distance target values: 2.64, 5.5 (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

Keywords BAD-1, PROTEIN, repeat