BMRBj - BMREntryMaster

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BMRB: 30605

6OQJ

SOLUTION STRUCTURE OF THE COMPLEX OF MUTANT VEK50[RH1/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 ELQRLKNEAA EEAELERLKS ERHDHDKKEA 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: 99.3 %, Completeness: 91.0 %, Completeness (bb): 97.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.0 % (1481 of 1627)	89.3 % (770 of 862)	91.9 % (570 of 620)	97.2 % (141 of 145)
Backbone	97.2 % (797 of 820)	94.6 % (262 of 277)	98.5 % (405 of 411)	98.5 % (130 of 132)
Sidechain	86.8 % (816 of 940)	86.8 % (508 of 585)	86.8 % (297 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	92.4 % (85 of 92)	91.3 % (42 of 46)	93.5 % (43 of 46)

1. entity 1

YVEFSEECMH GSGENYDGKI SKTMSGLECQ AWDSQSPHAH GYIPSKFPNK NLKKNYCRNP DRDLRPWCFT TDPNKRWEYC DIPRCAA

2. entity 2

GSVEKLTADA ELQRLKNEAA EEAELERLKS ERHDHDKKEA 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[RH1/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 mM
2	VEK50[RH1/AA]	natural abundance	1.0 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 mM [U-99% 13C; U-99% 15N] VEK50[RH1/AA], 1 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 mM
7	VEK50[RH1/AA]	[U-99% 13C; U-99% 15N]	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

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	direct	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	nitrogen	internal	direct	0.1013291

Referencing offset: -0.28 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	direct	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	nitrogen	internal	direct	0.1013291

Referencing offset: -0.28 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	direct	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	nitrogen	internal	direct	0.1013291

Referencing offset: 0.19 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	direct	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	nitrogen	internal	direct	0.1013291

Referencing offset: -3.04 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 6OQJ, 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 : 3 entities Detail

Experiments performed 8 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[RH1/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 mM
2	VEK50[RH1/AA]	natural abundance	1.0 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 mM [U-99% 13C; U-99% 15N] VEK50[RH1/AA], 1 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 mM
7	VEK50[RH1/AA]	[U-99% 13C; U-99% 15N]	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 mM
7	VEK50[RH1/AA]	[U-99% 13C; U-99% 15N]	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
6	plasminogen kringle 2	natural abundance	1 mM
7	VEK50[RH1/AA]	[U-99% 13C; U-99% 15N]	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

5 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	plasminogen kringle 2	natural abundance	1 mM
7	VEK50[RH1/AA]	[U-99% 13C; U-99% 15N]	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 mM
7	VEK50[RH1/AA]	[U-99% 13C; U-99% 15N]	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 mM
7	VEK50[RH1/AA]	[U-99% 13C; U-99% 15N]	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 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 mM
2	VEK50[RH1/AA]	natural abundance	1.0 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	bmr30605_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 42.93 ppm	oxidized, CA 54.17, CB 39.5 ppm	n/a
1:29:CYS:SG	1:68:CYS:SG	oxidized, CA 55.14, CB 37.59 ppm	oxidized, CA 55.86, CB 42.1 ppm	n/a
1:57:CYS:SG	1:80:CYS:SG	oxidized, CA 59.824, CB 48.36 ppm	oxidized, CA 54.618, CB 46.5 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr30605_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1570		98.9 (chain: 1, length: 87), 100.0 (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: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 855
  - ¹³C chemical shifts: 569
  - ¹⁵N chemical shifts: 146
- 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	229	71.8
¹³C chemical shifts	228	187	82.0
¹⁵N chemical shifts	58	51	87.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	105	95	90.5
¹³C chemical shifts	104	102	98.1
¹⁵N chemical shifts	52	51	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	214	134	62.6
¹³C chemical shifts	124	85	68.5
¹⁵N chemical shifts	6	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	20	80.0
¹³C chemical shifts	25	22	88.0

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

Keywords BLOOD CLOTTING, PLASMINOGEN BINDING PROTEIN, PROTEIN BINDING

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Found 1 Document (0.74 seconds)

BMRB: 30605

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

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

Related entities 2. M protein, entity 2, : 1 : 1 : 7 : 3 entities Detail

Experiments performed 8 experiments Detail

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Chemical shift validation 4 contents Detail