BMRBj - BMREntryMaster

Found 1 Document (0.862 seconds)

BMRB: 30686

6BZJ

Solution structure of AGL55-Kringle 2 complex

Authors

Qiu, C., Yuan, Y., Castellino, F.J.

Assembly

M protein

Entity

1. M protein, entity 1 (polymer, Thiol state: all disulfide bound), 87 monomers, 10151.22 Da Detail

YVEFSEECMH GSGENYDGKI SKTMSGLECQ AWDSQSPHAH GYIPSKFPNK NLKKNYCRNP DRDLRPWCFT TDPNKRWEYC DIPRCAA

2. M protein, entity 2 (polymer, Thiol state: not present), 57 monomers, 6726.266 Da Detail

GSAGLQEKER ELEDLKDAEL KRLNEERHDH DKREAERKAL EDKLADKQEH LDGALRY

Total weight

16877.486 Da

Max. entity weight

10151.22 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS8:SG	1:CYS85:SG
2	disulfide	sing	1:CYS29:SG	1:CYS68:SG
3	disulfide	sing	1:CYS57:SG	1:CYS80:SG

Source organism

Homo sapiens , Streptococcus pyogenes NS88.2

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 40.3 %, Completeness: 33.3 %, Completeness (bb): 39.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	33.3 % (569 of 1708)	31.9 % (288 of 903)	35.3 % (227 of 643)	33.3 % (54 of 162)
Backbone	39.2 % (333 of 850)	37.7 % (109 of 289)	40.1 % (170 of 424)	39.4 % (54 of 137)
Sidechain	29.3 % (291 of 994)	29.2 % (179 of 614)	31.5 % (112 of 355)	0.0 % (0 of 25)
Aromatic	0.0 % (0 of 138)	0.0 % (0 of 69)	0.0 % (0 of 66)	0.0 % (0 of 3)
Methyl	48.9 % (44 of 90)	53.3 % (24 of 45)	44.4 % (20 of 45)

1. entity 1

YVEFSEECMH GSGENYDGKI SKTMSGLECQ AWDSQSPHAH GYIPSKFPNK NLKKNYCRNP DRDLRPWCFT TDPNKRWEYC DIPRCAA

2. entity 2

GSAGLQEKER ELEDLKDAEL KRLNEERHDH DKREAERKAL EDKLADKQEH LDGALRY

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 1.0 mM [U-99% 13C; U-99% 15N] AGL55, 1.2 mM Kringle 2, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	AGL55	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	Kringle 2	natural abundance	1.2 (±0.1) mM
3	Bis-Tris-d19	[U-2H]	20 mM
4	DSS	natural abundance	2 ug/mL
5	sodium azide	natural abundance	2 ug/mL

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 1.0 mM [U-99% 13C; U-99% 15N] Kringle 2, 1.2 mM AGL55, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	AGL55	natural abundance	1.2 (±0.1) mM
7	Kringle 2	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
8	Bis-Tris-d19	[U-2H]	20 mM
9	DSS	natural abundance	2 ug/mL
10	sodium azide	natural abundance	2 ug/mL

Protein Blocks Logo

Calculated from 20 models in PDB: 6UZ4, Strand ID: A, B Detail

Release date

2020-01-23

Citation

Structural evolution of the A-domain in plasminogen-binding Group A streptococcal M-protein reflects improved adaptability of the pathogen to the host
Qiu, C., Yuan, Y., Ploplis, V.A., Castellino, F.J.

Related entities 1. M protein, entity 1, : 116 entities Detail

Related entities 2. M protein, entity 2, : 1 : 1 : 27 entities Detail

Experiments performed 13 experiments Detail

1 2D TROSY-[1H-15N] HSQC

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 1.0 mM [U-99% 13C; U-99% 15N] AGL55, 1.2 mM Kringle 2, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	AGL55	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	Kringle 2	natural abundance	1.2 (±0.1) mM
3	Bis-Tris-d19	[U-2H]	20 mM
4	DSS	natural abundance	2 ug/mL
5	sodium azide	natural abundance	2 ug/mL

2 3D TROSY-HNCO

Instrument

Bruker AVANCE - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AGL55	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	Kringle 2	natural abundance	1.2 (±0.1) mM
3	Bis-Tris-d19	[U-2H]	20 mM
4	DSS	natural abundance	2 ug/mL
5	sodium azide	natural abundance	2 ug/mL

3 3D TROSY-HN(CA)CO

Instrument

Bruker AVANCE - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AGL55	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	Kringle 2	natural abundance	1.2 (±0.1) mM
3	Bis-Tris-d19	[U-2H]	20 mM
4	DSS	natural abundance	2 ug/mL
5	sodium azide	natural abundance	2 ug/mL

4 3D TROSY-HNCACB

Instrument

Bruker AVANCE - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AGL55	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	Kringle 2	natural abundance	1.2 (±0.1) mM
3	Bis-Tris-d19	[U-2H]	20 mM
4	DSS	natural abundance	2 ug/mL
5	sodium azide	natural abundance	2 ug/mL

5 3D TROSY-C(CO)NH

Instrument

Bruker AVANCE - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AGL55	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	Kringle 2	natural abundance	1.2 (±0.1) mM
3	Bis-Tris-d19	[U-2H]	20 mM
4	DSS	natural abundance	2 ug/mL
5	sodium azide	natural abundance	2 ug/mL

6 3D TROSY-HBHA(CBCA)NH

Instrument

Bruker AVANCE - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AGL55	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	Kringle 2	natural abundance	1.2 (±0.1) mM
3	Bis-Tris-d19	[U-2H]	20 mM
4	DSS	natural abundance	2 ug/mL
5	sodium azide	natural abundance	2 ug/mL

7 3D TROSY-H(CCO)NH

Instrument

Bruker AVANCE - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AGL55	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	Kringle 2	natural abundance	1.2 (±0.1) mM
3	Bis-Tris-d19	[U-2H]	20 mM
4	DSS	natural abundance	2 ug/mL
5	sodium azide	natural abundance	2 ug/mL

8 2D NOESY

Instrument

Bruker AVANCE - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AGL55	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	Kringle 2	natural abundance	1.2 (±0.1) mM
3	Bis-Tris-d19	[U-2H]	20 mM
4	DSS	natural abundance	2 ug/mL
5	sodium azide	natural abundance	2 ug/mL

9 3D NOESY

Instrument

Bruker AVANCE - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	AGL55	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	Kringle 2	natural abundance	1.2 (±0.1) mM
3	Bis-Tris-d19	[U-2H]	20 mM
4	DSS	natural abundance	2 ug/mL
5	sodium azide	natural abundance	2 ug/mL

10 2D IPAP

Instrument

Bruker AVANCE - 800 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 1.0 mM [U-99% 13C; U-99% 15N] AGL55, 1.2 mM Kringle 2, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	AGL55	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	Kringle 2	natural abundance	1.2 (±0.1) mM
3	Bis-Tris-d19	[U-2H]	20 mM
4	DSS	natural abundance	2 ug/mL
5	sodium azide	natural abundance	2 ug/mL

11 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 1.0 mM [U-99% 13C; U-99% 15N] Kringle 2, 1.2 mM AGL55, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	AGL55	natural abundance	1.2 (±0.1) mM
7	Kringle 2	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
8	Bis-Tris-d19	[U-2H]	20 mM
9	DSS	natural abundance	2 ug/mL
10	sodium azide	natural abundance	2 ug/mL

12 3D NOESY

Instrument

Bruker AVANCE - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	AGL55	natural abundance	1.2 (±0.1) mM
7	Kringle 2	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
8	Bis-Tris-d19	[U-2H]	20 mM
9	DSS	natural abundance	2 ug/mL
10	sodium azide	natural abundance	2 ug/mL

13 2D IPAP

Instrument

Bruker AVANCE - 800 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 1.0 mM [U-99% 13C; U-99% 15N] Kringle 2, 1.2 mM AGL55, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	AGL55	natural abundance	1.2 (±0.1) mM
7	Kringle 2	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
8	Bis-Tris-d19	[U-2H]	20 mM
9	DSS	natural abundance	2 ug/mL
10	sodium azide	natural abundance	2 ug/mL

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30686_3.str
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	OK

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:8:CYS:SG	1:85:CYS:SG	unknown	unknown	n/a
1:29:CYS:SG	1:68:CYS:SG	unknown	unknown	n/a
1:57:CYS:SG	1:80:CYS:SG	unknown	unknown	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr30686_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	605		98.2 (chain: 2, length: 57)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 2, Chain length: 57, Sequence coverage: 98.2%
- Total number of assignments
  - ¹H chemical shifts: 333
  - ¹³C chemical shifts: 220
  - ¹⁵N chemical shifts: 52
- Completeness of assignments
  - Entity_assemble_ID: 2
- 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: 2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	360	285	79.2
¹³C chemical shifts	251	220	87.6
¹⁵N chemical shifts	66	52	78.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	117	106	90.6
¹³C chemical shifts	114	110	96.5
¹⁵N chemical shifts	57	52	91.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	243	179	73.7
¹³C chemical shifts	137	110	80.3
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	24	100.0
¹³C chemical shifts	24	20	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	0	0.0
¹³C chemical shifts	10	0	0.0

Keywords PROTEIN BINDING, Plasminogen binding peptide

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Found 1 Document (0.862 seconds)

BMRB: 30686

Sample #1

Sample #2

Related entities 1. M protein, entity 1, : 116 entities Detail

Related entities 2. M protein, entity 2, : 1 : 1 : 27 entities Detail

Experiments performed 13 experiments Detail

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Chemical shift validation 4 contents Detail