PDB-2oto: N-terminal fragment of Streptococcus pyogenes M1 protein

ID or keywords:

Entry

Database: PDB / ID: 2oto

Title

N-terminal fragment of Streptococcus pyogenes M1 protein

Components

M protein

Keywords

SURFACE ACTIVE PROTEIN / TOXIN / helical coiled coil / fibrinogen-binding / virulence factor

Function / homology

Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #700 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / :

Function and homology information

Biological species

Streptococcus pyogenes serotype M1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 3.04 Å

Authors

McNamara, C.W. / Ghosh, P.

Citation

Journal: Science / Year: 2008
Title: Coiled-coil irregularities and instabilities in group A Streptococcus M1 are required for virulence.
Authors: McNamara, C. / Zinkernagel, A.S. / Macheboeuf, P. / Cunningham, M.W. / Nizet, V. / Ghosh, P.

History

Deposition	Feb 8, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 18, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.3	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

Remark 999

SEQUENCE The residue is a modified residue and an initiating methionine

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2oto.cif.gz	114.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2oto.ent.gz	91 KB	Display	PDB format
PDBx/mmJSON format	2oto.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2oto_validation.pdf.gz	453.4 KB	Display	wwPDB validaton report
Full document	2oto_full_validation.pdf.gz	494.9 KB	Display
Data in XML	2oto_validation.xml.gz	28.6 KB	Display
Data in CIF	2oto_validation.cif.gz	36.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ot/2oto ftp://data.pdbj.org/pub/pdb/validation_reports/ot/2oto	HTTPS FTP

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Related structure data

Similar structure data	5bu8-2 3wqa-d 6pgw-d 5to5-d 3tiq-2 5tvb-d 4cpc-2 6vfq-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: M protein

B: M protein

C: M protein

D: M protein

72.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: M protein

B: M protein

defined by author&software
36.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: M protein

D: M protein

defined by author&software
36.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	119.374, 83.405, 93.467
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	M protein Mass: 18181.918 Da / Num. of mol.: 4 / Fragment: residues 42-194 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria) Species: Streptococcus pyogenes / Strain: M1T1 strain 5448 / Gene: emm1.0 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q48WD8
Has protein modification	Y

#1: Protein

M protein

Mass: 18181.918 Da / Num. of mol.: 4 / Fragment: residues 42-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptococcus pyogenes serotype M1 (bacteria)
Species: Streptococcus pyogenes / Strain: M1T1 strain 5448 / Gene: emm1.0 / Plasmid: pET28b / Production host:

Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q48WD8

Has protein modification

Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 3.2 Å³/Da / Density % sol: 61.54 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: 32% MPD, 0.3M ammonium acetate, 0.1M sodium citrate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3		1
4		1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ALS	5.0.2	1	0.97929,0.97945,0.95666,1.008
SYNCHROTRON	APS	19-ID	2	0.97934

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315	1	CCD	Jun 10, 2005
ADSC QUANTUM 315	2	CCD	Nov 13, 2004

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	double-crystal, Si(111)	MAD	M	x-ray	1
2	double-crystal, sagitally focused Si(111)	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97929	1
2	0.97945	1
3	0.95666	1
4	1.008	1
5	0.97934	1

Reflection

D res low: 50 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	D res high (Å)	Num. obs	% possible obs
7	1	9.1	277967	0.098	1.02	2.81	39832	90.8
3.6	2	9.3	127147	0.091	1	2.9	35183	87.4
3.6	3	7.9	121837	0.099	1	2.9	34170	84.8
3.5	4	10.2	131241	0.099	1	2.78	37184	82.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.05	50	96.9	1	0.048	1.047	7.5
4.8	6.05	99.9	1	0.093	1.038	7.6
4.2	4.8	100	1	0.089	1.017	7.7
3.81	4.2	99.9	1	0.114	0.996	7.7
3.54	3.81	99.7	1	0.175	1.004	7.4
3.33	3.54	98.8	1	0.279	1.028	7
3.16	3.33	91.9	1	0.3	1.007	6.7
3.03	3.16	82.8	1	0.313	1.003	6.3
2.91	3.03	74.6	1	0.365	1.001	5.7
2.81	2.91	64	1	0.523	0.999	5.1
6.24	50	98.7	2	0.051	1.037	3.8
4.96	6.24	100	2	0.088	0.983	3.9
4.33	4.96	100	2	0.079	0.984	3.9
3.94	4.33	99	2	0.101	0.991	3.8
3.65	3.94	95.7	2	0.131	1.003	3.7
3.44	3.65	90.5	2	0.221	0.998	3.6
3.27	3.44	83.7	2	0.298	1.012	3.5
3.12	3.27	75.8	2	0.293	0.997	3.4
3	3.12	68.3	2	0.301	1.007	3.3
2.9	3	62.5	2	0.351	0.987	3
6.24	50	99.5	3	0.051	0.946	3.8
4.96	6.24	100	3	0.095	0.983	3.8
4.33	4.96	99.9	3	0.087	0.997	3.8
3.94	4.33	98	3	0.116	1.029	3.7
3.65	3.94	92.2	3	0.157	0.997	3.6
3.44	3.65	86.6	3	0.281	1.005	3.6
3.27	3.44	80.1	3	0.392	1.005	3.5
3.12	3.27	72.1	3	0.375	1.007	3.3
3	3.12	63.9	3	0.356	1	3.1
2.9	3	55.5	3	0.393	0.993	2.8
5.99	50	94.4	4	0.056	0.993	3.7
4.75	5.99	99.3	4	0.087	1.012	3.8
4.15	4.75	99.8	4	0.094	0.978	3.8
3.77	4.15	99.8	4	0.123	1.037	3.7
3.5	3.77	97	4	0.184	1.016	3.6
3.3	3.5	91.3	4	0.28	0.993	3.5
3.13	3.3	79.5	4	0.253	1.01	3.4
2.99	3.13	67.4	4	0.256	0.999	3.2
2.88	2.99	55.4	4	0.284	1.009	2.9
2.78	2.88	41.9	4	0.427	0.992	2.9

Reflection

Resolution: 3.03→50 Å / Num. all: 18650 / Num. obs: 18530 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / B_iso Wilson estimate: 72.5 Å² / R_merge(I) obs: 0.076 / Χ²: 1.002 / Net I/σ(I): 7.9

Reflection shell

Resolution: 3.03→3.14 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.376 / Num. unique all: 1796 / Χ²: 1.001 / % possible all: 98.5

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3
4

Phasing MAD

D res high: 3.18 Å / D res low: 50 Å / FOM : 0.51 / Reflection: 15154

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	4 wavelength	1	0.9793	4.6	-8.3
1	4 wavelength	2	0.9794	2.5	-10.1
1	4 wavelength	3	0.9567	3.7	-3
1	4 wavelength	4	1.008	0.53	-3.1

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	60	0.182	0.104	0.253	1.095
2	Se	60	0.508	0.449	0.273	0.987
3	Se	60	0.482	0.198	0.306	1.043
4	Se	60	0.015	0.164	0.184	0.604
5	Se	60	0.659	0.043	0.263	0.803
6	Se	60	0.31	0.316	0.301	0.559
7	Se	60	0.282	0.219	0.29	0.548

Phasing MAD shell

Resolution (Å)	FOM	Reflection
11.43-50	0.62	813
7.22-11.43	0.73	1363
5.65-7.22	0.66	1698
4.79-5.65	0.6	1997
4.23-4.79	0.54	2209
3.83-4.23	0.47	2367
3.53-3.83	0.39	2412
3.28-3.53	0.27	2295

Phasing dm

FOM : 0.59 / FOM acentric: 0.58 / FOM centric: 0.65 / Reflection: 17195 / Reflection acentric: 15103 / Reflection centric: 2092

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
8.6-48.578	0.92	0.92	0.91	895	624	271
5.4-8.6	0.81	0.82	0.78	2629	2151	478
4.3-5.4	0.76	0.76	0.7	3191	2778	413
3.8-4.3	0.65	0.66	0.61	3123	2794	329
3.2-3.8	0.44	0.43	0.47	4923	4517	406
3-3.2	0.22	0.21	0.29	2434	2239	195

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.09	phasing
RESOLVE	2.09	phasing
REFMAC	refmac_5.2.0005	refinement
PDB_EXTRACT	2	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 3.04→40.76 Å / Cor.coef. F_o:F_c: 0.9 / Cor.coef. F_o:F_c free: 0.905 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.534 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.338	963	5.2 %	RANDOM
R_work	0.337	-	-	-
all	0.337	18530	-	-
obs	0.337	18433	99.34 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 92.554 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.26 Å²	0 Å²	0 Å²
2-	-	15.26 Å²	0 Å²
3-	-	-	-15.53 Å²

Refinement step

Cycle: LAST / Resolution: 3.04→40.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4521	0	0	0	4521

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	4557
X-RAY DIFFRACTION	r_angle_refined_deg	1.361	1.985	6084
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.864	5	544
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.38	25.72	271
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.987	15	983
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.82	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	652
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3436
X-RAY DIFFRACTION	r_nbd_refined	0.324	0.2	2814
X-RAY DIFFRACTION	r_nbtor_refined	0.317	0.2	3072
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.227	0.2	343
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.477	0.2	48
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.558	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	20.793	4	2740
X-RAY DIFFRACTION	r_mcangle_it	28.202	6	4343
X-RAY DIFFRACTION	r_scbond_it	2.317	7	1817
X-RAY DIFFRACTION	r_scangle_it	2.367	10	1741

LS refinement shell

Resolution: 3.04→3.119 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.566	92	-
R_work	0.535	1224	-
obs	-	1316	98.14 %

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