BMRBj - BMREntryMaster

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BMRB: 30606

6OKY

SOLUTION STRUCTURE OF THE COMPLEX OF MUTANT VEK50[RH2/AA] AND PLASMINOGEN KRINGLE 2

Authors

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), 52 monomers, 6007.500 Da Detail

GSVEKLTADA ELQRLKNERH EEAELERLKS EAADHDKKEA ERKALEDKLA DY

Total weight

16158.72 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

Exptl. method

solution NMR

Refine. method

simulated annealingsimulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 91.5 %, Completeness (bb): 97.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.5 % (1488 of 1627)	89.2 % (769 of 862)	93.2 % (578 of 620)	97.2 % (141 of 145)
Backbone	97.4 % (799 of 820)	96.0 % (266 of 277)	98.1 % (403 of 411)	98.5 % (130 of 132)
Sidechain	87.3 % (821 of 940)	86.0 % (503 of 585)	89.8 % (307 of 342)	84.6 % (11 of 13)
Aromatic	81.3 % (109 of 134)	82.1 % (55 of 67)	79.7 % (51 of 64)	100.0 % (3 of 3)
Methyl	96.7 % (89 of 92)	93.5 % (43 of 46)	100.0 % (46 of 46)

1. entity 1

YVEFSEECMH GSGENYDGKI SKTMSGLECQ AWDSQSPHAH GYIPSKFPNK NLKKNYCRNP DRDLRPWCFT TDPNKRWEYC DIPRCAA

2. entity 2

GSVEKLTADA ELQRLKNERH EEAELERLKS EAADHDKKEA ERKALEDKLA DY

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 1.0 mM [U-99% 13C; U-99% 15N] plasminogen Kringle 2, 1.0 mM VEK50[RH2/AA], 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	plasminogen Kringle 2	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	VEK50[RH2/AA]	natural abundance	1.0 (±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 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 1.0 mM [U-99% 13C; U-99% 15N] VEK50[RH2/AA], 1.0 mM plasminogen Kringle 2, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	plasminogen Kringle 2	natural abundance	1.0 (±0.1) mM
7	VEK50[RH2/AA]	[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 10 models in PDB: 6OQK, Strand ID: A, B Detail

Release date

2019-05-02

Citation

Solution structural model of the complex of the binding regions of human plasminogen with its M-protein receptor from Streptococcus pyogenes
Yuan, Y., Ayinuola, Y.A., Singh, D., Ayinuola, O., Mayfield, J.A., Quek, A., Whisstock, J.C., Law, R., Lee, S.W., Ploplis, V.A., Castellino, F.J.
J. Struct. Biol. (2019), 208, 18-29, PubMed 31301349 , DOI 10.1016/j.jsb.2019.07.005 , Abstract

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

Related entities 2. M protein, entity 2, : 1 : 1 : 7 : 5 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 1.0 mM [U-99% 13C; U-99% 15N] plasminogen Kringle 2, 1.0 mM VEK50[RH2/AA], 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	plasminogen Kringle 2	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	VEK50[RH2/AA]	natural abundance	1.0 (±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 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 1.0 mM [U-99% 13C; U-99% 15N] VEK50[RH2/AA], 1.0 mM plasminogen Kringle 2, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	plasminogen Kringle 2	natural abundance	1.0 (±0.1) mM
7	VEK50[RH2/AA]	[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

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	plasminogen Kringle 2	natural abundance	1.0 (±0.1) mM
7	VEK50[RH2/AA]	[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

4 3D C(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	plasminogen Kringle 2	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	VEK50[RH2/AA]	natural abundance	1.0 (±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 C(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	plasminogen Kringle 2	natural abundance	1.0 (±0.1) mM
7	VEK50[RH2/AA]	[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

6 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	plasminogen Kringle 2	natural abundance	1.0 (±0.1) mM
7	VEK50[RH2/AA]	[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

7 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	plasminogen Kringle 2	natural abundance	1.0 (±0.1) mM
7	VEK50[RH2/AA]	[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

8 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	plasminogen Kringle 2	natural abundance	1.0 (±0.1) mM
7	VEK50[RH2/AA]	[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

9 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	plasminogen Kringle 2	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	VEK50[RH2/AA]	natural abundance	1.0 (±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 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	plasminogen Kringle 2	natural abundance	1.0 (±0.1) mM
7	VEK50[RH2/AA]	[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

11 3D NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	plasminogen Kringle 2	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
2	VEK50[RH2/AA]	natural abundance	1.0 (±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

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30606_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	Warning

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	oxidized, CA 53.88, CB 43.144 ppm	oxidized, CA 54.177, CB 39.574 ppm	n/a
1:29:CYS:SG	1:68:CYS:SG	oxidized, CA 55.189, CB 37.938 ppm	oxidized, CA 55.876, CB 42.232 ppm	n/a
1:57:CYS:SG	1:80:CYS:SG	oxidized, CA 59.824, CB 48.356 ppm	oxidized, CA 54.618, CB 46.736 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr30606_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1602		98.9 (chain: 1, length: 87), 98.1 (chain: 2, length: 52)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 87, Sequence coverage: 98.9%
  - Entity_assembly_ID: 2, Chain length: 52, Sequence coverage: 98.1%
- Total number of assignments
  - ¹H chemical shifts: 878
  - ¹³C chemical shifts: 579
  - ¹⁵N chemical shifts: 145
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
- Redox state of CYS
- Peptide bond of PRO
- 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: 1
  - Chain_ID: 2

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
10	HIS	HD1	7.298
10	HIS	HE2	9.569
16	TYR	HH	10.642
23	THR	HG1	6.051
25	SER	HG	6.06
34	SER	HG	6.173
36	SER	HG	5.346
40	HIS	HE2	10.346
45	SER	HG	4.835
70	THR	HG1	6.205
71	THR	HG1	6.203

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	543	533	98.2
¹³C chemical shifts	392	382	97.4
¹⁵N chemical shifts	96	95	99.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	172	170	98.8
¹³C chemical shifts	174	172	98.9
¹⁵N chemical shifts	80	79	98.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	371	363	97.8
¹³C chemical shifts	218	210	96.3
¹⁵N chemical shifts	16	16	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	21	91.3
¹³C chemical shifts	23	21	91.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	55	93.2
¹³C chemical shifts	56	51	91.1
¹⁵N chemical shifts	3	3	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	319	248	77.7
¹³C chemical shifts	228	197	86.4
¹⁵N chemical shifts	58	50	86.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	105	100	95.2
¹³C chemical shifts	104	101	97.1
¹⁵N chemical shifts	52	50	96.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	214	148	69.2
¹³C chemical shifts	124	96	77.4
¹⁵N chemical shifts	6	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	22	88.0
¹³C chemical shifts	25	25	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	0	0.0
¹³C chemical shifts	8	0	0.0

Keywords PROTEIN BINDING, Plasminogen binding peptide, blood clotting

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Found 1 Document (0.802 seconds)

BMRB: 30606

Sample #1

Sample #2

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

Related entities 2. M protein, entity 2, : 1 : 1 : 7 : 5 entities Detail

Experiments performed 11 experiments Detail

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Chemical shift validation 4 contents Detail