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BMRB: 30313

5WAH

SOLUTION NMR STRUCTURE OF SIGLEC-5 BINDING DOMAIN FROM STREPTOCOCCAL BETA PROTEIN

Authors

Eletsky, A., Chen, C., Fong, J.J., Nizet, V., Varki, A., Prestegard, J.H.

Assembly

IgA FC receptor

Entity

1. IgA FC receptor (polymer, Thiol state: not present), 99 monomers, 11492.49 Da Detail

GVEKTAGETS ATDTGKREKQ LQQWKNNLKN DVDNTILSHE QKNEFKTKID ETNDSDALLE LENQFNETNR LLHIKQHEEV EKDKKAKQQK TLKQSDTKV

Formula weight

11492.49 Da

Source organism

Streptococcus agalactiae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 99.0 %, Completeness: 98.8 %, Completeness (bb): 98.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.8 % (1181 of 1195)	98.9 % (628 of 635)	98.6 % (436 of 442)	99.2 % (117 of 118)
Backbone	98.8 % (587 of 594)	98.0 % (197 of 201)	99.3 % (292 of 294)	99.0 % (98 of 99)
Sidechain	99.0 % (690 of 697)	99.3 % (431 of 434)	98.4 % (240 of 244)	100.0 % (19 of 19)
Aromatic	90.9 % (40 of 44)	100.0 % (22 of 22)	81.0 % (17 of 21)	100.0 % (1 of 1)
Methyl	100.0 % (92 of 92)	100.0 % (46 of 46)	100.0 % (46 of 46)

1. entity 1

GVEKTAGETS ATDTGKREKQ LQQWKNNLKN DVDNTILSHE QKNEFKTKID ETNDSDALLE LENQFNETNR LLHIKQHEEV EKDKKAKQQK TLKQSDTKV

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 6.5, Details 0.45 mM [U-13C; U-15N] IgA-Fc Receptor, 20 mM sodium phosphate, 4 uM DSS, 0.01 % sodium azide, 100 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	4 uM
2	IgA-Fc Receptor	[U-13C; U-15N]	0.45 mM
3	sodium azide	natural abundance	0.01 %
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 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: 0.01 ppm, Outliers: 1 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: 0.01 ppm, Outliers: 1 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: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

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: -0.26 ppm, Outliers: 1 Detail

Release date

2017-08-03

Citation

SOLUTION NMR STRUCTURE OF SIGLEC-5 BINDING DOMAIN FROM STREPTOCOCCAL BETA PROTEIN
Eletsky, A., Chen, C., Fong, J.J., Nizet, V., Varki, A., Prestegard, J.H.

Related entities 1. IgA FC receptor, : 1 : 1 : 1 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent DD2 - 900 MHz 5MM CRYOGENIC PROBE

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 6.5, Details 0.45 mM [U-13C; U-15N] IgA-Fc Receptor, 20 mM sodium phosphate, 4 uM DSS, 0.01 % sodium azide, 100 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	4 uM
2	IgA-Fc Receptor	[U-13C; U-15N]	0.45 mM
3	sodium azide	natural abundance	0.01 %
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

2 2D 1H-13C CT-HSQC aliphatic

Instrument

Agilent DD2 - 900 MHz 5MM CRYOGENIC PROBE

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	4 uM
2	IgA-Fc Receptor	[U-13C; U-15N]	0.45 mM
3	sodium azide	natural abundance	0.01 %
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

3 2D 1H-13C CT-HSQC aromatic

Instrument

Agilent DD2 - 900 MHz 5MM CRYOGENIC PROBE

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	4 uM
2	IgA-Fc Receptor	[U-13C; U-15N]	0.45 mM
3	sodium azide	natural abundance	0.01 %
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

4 3D HNCO

Instrument

Agilent DD2 - 600 MHz 3MM CRYOGENIC PROBE

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	4 uM
2	IgA-Fc Receptor	[U-13C; U-15N]	0.45 mM
3	sodium azide	natural abundance	0.01 %
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

5 3D CBCA(CO)NH

Instrument

Varian VNMRS - 600 MHz 5MM CRYOGENIC PROBE

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	4 uM
2	IgA-Fc Receptor	[U-13C; U-15N]	0.45 mM
3	sodium azide	natural abundance	0.01 %
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

6 3D 1H-15N NOESY

Instrument

Agilent DD2 - 800 MHz 5MM CRYOGENIC PROBE

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	4 uM
2	IgA-Fc Receptor	[U-13C; U-15N]	0.45 mM
3	sodium azide	natural abundance	0.01 %
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

7 3D HNCACB

Instrument

Agilent DD2 - 600 MHz 3MM CRYOGENIC PROBE

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	4 uM
2	IgA-Fc Receptor	[U-13C; U-15N]	0.45 mM
3	sodium azide	natural abundance	0.01 %
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

8 3D HCCH-TOCSY aliphatic

Instrument

Agilent DD2 - 900 MHz 5MM CRYOGENIC PROBE

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	4 uM
2	IgA-Fc Receptor	[U-13C; U-15N]	0.45 mM
3	sodium azide	natural abundance	0.01 %
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

9 3D HCCH-COSY aromatic

Instrument

Agilent DD2 - 800 MHz 5MM CRYOGENIC PROBE

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	4 uM
2	IgA-Fc Receptor	[U-13C; U-15N]	0.45 mM
3	sodium azide	natural abundance	0.01 %
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

10 3D HCCH-COSY aliphatic

Instrument

Agilent DD2 - 800 MHz 5MM CRYOGENIC PROBE

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	4 uM
2	IgA-Fc Receptor	[U-13C; U-15N]	0.45 mM
3	sodium azide	natural abundance	0.01 %
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

11 3D HBHA(CO)NH

Instrument

Varian VNMRS - 600 MHz 5MM CRYOGENIC PROBE

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	4 uM
2	IgA-Fc Receptor	[U-13C; U-15N]	0.45 mM
3	sodium azide	natural abundance	0.01 %
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

12 3D (H)CA(CO)NH

Instrument

Agilent DD2 - 600 MHz 3MM CRYOGENIC PROBE

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	4 uM
2	IgA-Fc Receptor	[U-13C; U-15N]	0.45 mM
3	sodium azide	natural abundance	0.01 %
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

13 3D 1H-13C NOESY

Instrument

Agilent DD2 - 800 MHz 5MM CRYOGENIC PROBE

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	4 uM
2	IgA-Fc Receptor	[U-13C; U-15N]	0.45 mM
3	sodium azide	natural abundance	0.01 %
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30313_5wah.nef
Input source #2: Coordindates	5wah.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

--------10--------20--------30--------40--------50--------60--------70--------80--------90---------
GVEKTAGETSATDTGKREKQLQQWKNNLKNDVDNTILSHEQKNEFKTKIDETNDSDALLELENQFNETNRLLHIKQHEEVEKDKKAKQQKTLKQSDTKV
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GVEKTAGETSATDTGKREKQLQQWKNNLKNDVDNTILSHEQKNEFKTKIDETNDSDALLELENQFNETNRLLHIKQHEEVEKDKKAKQQKTLKQSDTKV

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	99	0	0	100.0

Content subtype: combined_30313_5wah.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1189		99.0 (chain: A, length: 99)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2011 (1)	noe	90.9 (chain: A, length: 99)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	165 (165)	.	71.7 (chain: A, length: 99)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 99.0%
- Total number of assignments
  - ¹H chemical shifts: 630
  - ¹³C chemical shifts: 436
  - ¹⁵N chemical shifts: 123
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
35	THR	HG1	5.544
39	HIS	ND1	214.688
39	HIS	NE2	178.266
52	THR	HG1	5.951
73	HIS	ND1	194.362
73	HIS	NE2	185.076
77	HIS	ND1	198.076
77	HIS	NE2	177.853

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	635	628	98.9
¹³C chemical shifts	442	436	98.6
¹⁵N chemical shifts	120	117	97.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	201	197	98.0
¹³C chemical shifts	198	196	99.0
¹⁵N chemical shifts	99	97	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	434	431	99.3
¹³C chemical shifts	244	240	98.4
¹⁵N chemical shifts	21	20	95.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	46	100.0
¹³C chemical shifts	46	46	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	22	100.0
¹³C chemical shifts	21	17	81.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 90.9%
- Total number of restraints: 2008
- Weight of restraints: 1.0 (2008)
- Potential type of restraints: square-well-parabolic (2008)
- Range of distance target values: 1.48, 2.89 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 71.7%
- Total number of restraints: 165
- Total number of restraints per polymer type: 165
- Weight of restraints: 1.0 (165)
- Potential type of restraints: square-well-parabolic (165)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords BETA ANTIGEN, IGA-FC RECEPTOR, PROTEIN BINDING, THREE-HELIX BUNDLE

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Found 1 Document (0.54 seconds)

BMRB: 30313

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. IgA FC receptor, : 1 : 1 : 1 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 4 contents Detail