PDB-3r8b: Crystal structure of Staphylococcal Enterotoxin B in complex with...

ID or keywords:

Entry

Database: PDB / ID: 3r8b

Title

Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8

Components

Enterotoxin type B
G5-8

Keywords

TOXIN/IMMUNE SYSTEM / immunoglobulin-like / OB-fold / TOXIN-IMMUNE SYSTEM complex

Function / homology

Function and homology information

toxin activity / extracellular region / metal ion binding
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.95 Å

Authors

Bonsor, D.A. / Sundberg, E.J.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Molecular basis of a million-fold affinity maturation process in a protein-protein interaction.
Authors: Bonsor, D.A. / Postel, S. / Pierce, B.G. / Wang, N. / Zhu, P. / Buonpane, R.A. / Weng, Z. / Kranz, D.M. / Sundberg, E.J.

History

Deposition	Mar 23, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 6, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Aug 10, 2011	Group: Database references
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3r8b.cif.gz	534 KB	Display	PDBx/mmCIF format
PDB format	pdb3r8b.ent.gz	436.8 KB	Display	PDB format
PDBx/mmJSON format	3r8b.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3r8b_validation.pdf.gz	568.1 KB	Display	wwPDB validaton report
Full document	3r8b_full_validation.pdf.gz	601.4 KB	Display
Data in XML	3r8b_validation.xml.gz	89 KB	Display
Data in CIF	3r8b_validation.cif.gz	123 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r8/3r8b ftp://data.pdbj.org/pub/pdb/validation_reports/r8/3r8b	HTTPS FTP

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Related structure data

Related structure data	2icwS 3sebS S: Starting model for refinement
Similar structure data	3byt-4 3owe-7 3mc0-2 3owe-3 3owe-4 5q4u-d 3owe-2 1n0l-1 3mc0-1 5q4k-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) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2icwS

3sebS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#69 - Sep 2005 Cholera Toxin similarity (1)

Deposited unit

A: Enterotoxin type B

B: G5-8

C: Enterotoxin type B

D: G5-8

E: Enterotoxin type B

F: G5-8

G: Enterotoxin type B

H: G5-8

I: Enterotoxin type B

J: G5-8

K: Enterotoxin type B

L: G5-8

M: Enterotoxin type B

N: G5-8

O: Enterotoxin type B

P: G5-8

hetero molecules

340 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Enterotoxin type B

B: G5-8

hetero molecules

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

2

C: Enterotoxin type B

D: G5-8

hetero molecules

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

3

E: Enterotoxin type B

F: G5-8

hetero molecules

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

4

G: Enterotoxin type B

H: G5-8

hetero molecules

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

5

I: Enterotoxin type B

J: G5-8

hetero molecules

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

6

K: Enterotoxin type B

L: G5-8

hetero molecules

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

7

M: Enterotoxin type B

N: G5-8

hetero molecules

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

8

O: Enterotoxin type B

P: G5-8

hetero molecules

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

Unit cell

Length a, b, c (Å)	109.954, 160.370, 186.265
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2

#1: Protein	Enterotoxin type B / SEB Mass: 28411.064 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: entB / Production host: Escherichia coli (E. coli) / References: UniProt: P01552
#2: Protein	G5-8 Mass: 13821.528 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	... ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.39 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium ...Details: Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal

Density Matthews: 2.43 Å³/Da / Density % sol: 49.39 %

Crystal grow

Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9537
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 4, 2010 / Details: TOROIDAL FOCUSING MIRROR
Radiation	Monochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.95→121.531 Å / Num. all: 69820 / Num. obs: 66122 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.9 % / R_sym value: 0.199 / Net I/σ(I): 16.75
Reflection shell	Resolution: 2.95→3.06 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 4.5 / R_sym value: 0.793 / % possible all: 99

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3SEB AND 2ICW

3seb

2icw

Resolution: 2.95→46.57 Å / Cor.coef. F_o:F_c: 0.896 / Cor.coef. F_o:F_c free: 0.878 / SU B: 19.399 / SU ML: 0.363 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.489 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26547	3244	5 %	RANDOM
R_work	0.24607	-	-	-
all	0.24705	66380	-	-
obs	0.24705	61375	92.46 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 37.936 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.56 Å²	0 Å²	0 Å²
2-	-	0.93 Å²	0 Å²
3-	-	-	0.62 Å²

Refinement step

Cycle: LAST / Resolution: 2.95→46.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21868	0	43	0	21911

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	22378
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	15152
X-RAY DIFFRACTION	r_angle_refined_deg	1.259	1.951	30192
X-RAY DIFFRACTION	r_angle_other_deg	0.852	3	36891
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.41	5	2668
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.167	24.728	1123
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.7	15	3911
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.196	15	84
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	3176
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	24840
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	4676
X-RAY DIFFRACTION	r_mcbond_it	0.518	1.5	13383
X-RAY DIFFRACTION	r_mcbond_other	0.08	1.5	5460
X-RAY DIFFRACTION	r_mcangle_it	1.009	2	21554
X-RAY DIFFRACTION	r_scbond_it	1.222	3	8995
X-RAY DIFFRACTION	r_scangle_it	2.119	4.5	8638

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	2435	tight positional	0.03	0.05
1	1	C	2435	tight positional	0.03	0.05
1	1	E	2435	tight positional	0.03	0.05
1	1	G	2435	tight positional	0.04	0.05
1	1	I	2435	tight positional	0.03	0.05
1	1	K	2435	tight positional	0.03	0.05
1	1	M	2435	tight positional	0.03	0.05
1	1	O	2435	tight positional	0.04	0.05
2	2	B	968	tight positional	0.04	0.05
2	2	D	968	tight positional	0.04	0.05
2	2	F	968	tight positional	0.04	0.05
2	2	H	968	tight positional	0.03	0.05
2	2	J	968	tight positional	0.04	0.05
2	2	L	968	tight positional	0.04	0.05
2	2	N	968	tight positional	0.04	0.05
2	2	P	968	tight positional	0.03	0.05
1	1	A	663	loose positional	0.03	5
1	1	C	663	loose positional	0.03	5
1	1	E	663	loose positional	0.03	5
1	1	G	663	loose positional	0.03	5
1	1	I	663	loose positional	0.03	5
1	1	K	663	loose positional	0.03	5
1	1	M	663	loose positional	0.03	5
1	1	O	663	loose positional	0.03	5
2	2	B	443	loose positional	0.03	5
2	2	D	443	loose positional	0.03	5
2	2	F	443	loose positional	0.04	5
2	2	H	443	loose positional	0.03	5
2	2	J	443	loose positional	0.04	5
2	2	L	443	loose positional	0.03	5
2	2	N	443	loose positional	0.03	5
2	2	P	443	loose positional	0.03	5
1	1	A	2435	tight thermal	0.08	0.5
1	1	C	2435	tight thermal	0.06	0.5
1	1	E	2435	tight thermal	0.07	0.5
1	1	G	2435	tight thermal	0.07	0.5
1	1	I	2435	tight thermal	0.06	0.5
1	1	K	2435	tight thermal	0.06	0.5
1	1	M	2435	tight thermal	0.06	0.5
1	1	O	2435	tight thermal	0.08	0.5
2	2	B	968	tight thermal	0.07	0.5
2	2	D	968	tight thermal	0.07	0.5
2	2	F	968	tight thermal	0.07	0.5
2	2	H	968	tight thermal	0.07	0.5
2	2	J	968	tight thermal	0.07	0.5
2	2	L	968	tight thermal	0.07	0.5
2	2	N	968	tight thermal	0.07	0.5
2	2	P	968	tight thermal	0.07	0.5
1	1	A	663	loose thermal	0.07	10
1	1	C	663	loose thermal	0.06	10
1	1	E	663	loose thermal	0.07	10
1	1	G	663	loose thermal	0.07	10
1	1	I	663	loose thermal	0.07	10
1	1	K	663	loose thermal	0.07	10
1	1	M	663	loose thermal	0.07	10
1	1	O	663	loose thermal	0.08	10
2	2	B	443	loose thermal	0.06	10
2	2	D	443	loose thermal	0.07	10
2	2	F	443	loose thermal	0.07	10
2	2	H	443	loose thermal	0.07	10
2	2	J	443	loose thermal	0.07	10
2	2	L	443	loose thermal	0.08	10
2	2	N	443	loose thermal	0.08	10
2	2	P	443	loose thermal	0.06	10

LS refinement shell

Resolution: 2.952→3.029 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.322	256	-
R_work	0.292	4687	-
obs	-	-	96.47 %

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