PDB-3sbc: Crystal structure of Saccharomyces cerevisiae TSA1C47S mutant protein

ID or keywords:

Entry

Database: PDB / ID: 3sbc

Title

Crystal structure of Saccharomyces cerevisiae TSA1C47S mutant protein

Components

Peroxiredoxin TSA1

Keywords

OXIDOREDUCTASE / Alpha-Beta Fold / Peroxidase / Cytosol

Function / homology

Function and homology information

: / : / : / : / : / kinase regulator activity / cellular response to hydroperoxide / thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / DNA protection ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Tairum Jr., C.A. / Horta, B.B. / Netto, L.E.S. / Oliveira, M.A.

Citation

Journal: J.Mol.Biol. / Year: 2012
Title: Disulfide biochemistry in 2-cys peroxiredoxin: requirement of Glu50 and Arg146 for the reduction of yeast Tsa1 by thioredoxin.
Authors: Tairum, C.A. / de Oliveira, M.A. / Horta, B.B. / Zara, F.J. / Netto, L.E.

History

Deposition	Jun 3, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 8, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 29, 2014	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	3sbc.cif.gz	377.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3sbc.ent.gz	309.6 KB	Display	PDB format
PDBx/mmJSON format	3sbc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3sbc_validation.pdf.gz	564.3 KB	Display	wwPDB validaton report
Full document	3sbc_full_validation.pdf.gz	638.9 KB	Display
Data in XML	3sbc_validation.xml.gz	78.7 KB	Display
Data in CIF	3sbc_validation.cif.gz	107.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sb/3sbc ftp://data.pdbj.org/pub/pdb/validation_reports/sb/3sbc	HTTPS FTP

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Related structure data

Similar structure data	1qmv-d 2pn8-d 3tks-1 3tkr-d 1zof-d 2z9s-d 7kiz-d 3tjf-1 7kj1-d 3tjk-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #166 - Oct 2013 Proteasome similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #219 - Mar 2018 Vacuolar ATPase similarity (1) #108 - Dec 2008 Hsp90 similarity (1) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #85 - Jan 2007 Importins similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

PDB pages

PDBj /

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NCBI

Related items in Molecule of the Month

#127 - Jul 2010
Crystallins
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#166 - Oct 2013
Proteasome
similarity (1)
#196 - Apr 2016
Lead Poisoning
similarity (1)
#219 - Mar 2018
Vacuolar ATPase
similarity (1)
#108 - Dec 2008
Hsp90
similarity (1)
#203 - Nov 2016
Aminopeptidase 1 and Autophagy
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#85 - Jan 2007
Importins
similarity (1)
#24 - Dec 2001
Glycogen Phosphorylase
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)

Deposited unit

A: Peroxiredoxin TSA1

B: Peroxiredoxin TSA1

C: Peroxiredoxin TSA1

D: Peroxiredoxin TSA1

E: Peroxiredoxin TSA1

F: Peroxiredoxin TSA1

G: Peroxiredoxin TSA1

H: Peroxiredoxin TSA1

I: Peroxiredoxin TSA1

J: Peroxiredoxin TSA1

hetero molecules

239 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	239.983, 51.961, 192.355
Angle α, β, γ (deg.)	90.00, 92.33, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	1 - 196
2	1	1	4	B	1 - 196
3	1	1	4	C	1 - 196
4	1	1	4	D	1 - 196
5	1	1	4	E	1 - 196
6	1	1	4	F	1 - 196
7	1	1	4	G	1 - 196
8	1	1	4	H	1 - 196
9	1	1	4	I	1 - 196
10	1	1	4	J	1 - 196

#1: Protein	Peroxiredoxin TSA1 / Cytoplasmic thiol peroxidase 1 / cTPx 1 / PRP / Thiol-specific antioxidant protein 1 / Thioredoxin peroxidase Mass: 23766.945 Da / Num. of mol.: 10 / Mutation: C47S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: BY4741 / Gene: TPX1, TSA, TSA1, YML028W, ZRG14 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P34760, peroxiredoxin
#2: Chemical	ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL Mass: 154.251 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₂S₂
#3: Chemical	ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₂S₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.21 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.1 M sodium citrate, 10% PEG 3000, 0.1 M sodium fluoride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 110 K

Diffraction source

Source:

SYNCHROTRON / Site:

LNLS

/ Beamline: D03B-MX1 / Wavelength: 1.43 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 14, 2007

Radiation

Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.43 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.937
1	1	-h,-k,l	2	0.063

Reflection

Resolution: 2.68→50 Å / Num. all: 58102 / Num. obs: 55115 / % possible obs: 94.8 % / Observed criterion σ(F): 10 / Observed criterion σ(I): 3.2 / Redundancy: 4 %

Reflection shell

Highest resolution: 2.798 Å / % possible all: 97.7

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
MOLREP		phasing
REFMAC	5.5.0110	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / Cor.coef. F_o:F_c: 0.914 / Cor.coef. F_o:F_c free: 0.838 / SU B: 33.773 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2735	2933	5.1 %	RANDOM
R_work	0.20153	-	-	-
obs	0.20517	55104	97.6 %	-
all	-	58102	-	-

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: 13.09 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.75 Å²	0 Å²	-0.51 Å²
2-	-	-0.64 Å²	0 Å²
3-	-	-	-0.16 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14991	0	48	352	15391

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	15415
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.783	1.962	21028
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.547	5	1949
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.31	24.962	659
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.868	15	2425
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.137	15	61
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	2447
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	11683
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.51	1.5	9749
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.985	2	15765
X-RAY DIFFRACTION	r_scbond_it	1.466	3	5666
X-RAY DIFFRACTION	r_scangle_it	2.602	4.5	5263
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 1431 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	medium positional	0.53	0.5
2	B	medium positional	0.76	0.5
3	C	medium positional	0.71	0.5
4	D	medium positional	0.6	0.5
5	E	medium positional	0.62	0.5
6	F	medium positional	0.58	0.5
7	G	medium positional	0.62	0.5
8	H	medium positional	0.53	0.5
9	I	medium positional	0.58	0.5
10	J	medium positional	0.58	0.5
1	A	medium thermal	1.63	2
2	B	medium thermal	0.95	2
3	C	medium thermal	0.97	2
4	D	medium thermal	1.31	2
5	E	medium thermal	0.7	2
6	F	medium thermal	1.43	2
7	G	medium thermal	1.07	2
8	H	medium thermal	0.87	2
9	I	medium thermal	0.86	2
10	J	medium thermal	0.96	2

LS refinement shell

Resolution: 2.8→2.873 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.45	202	-
R_work	0.342	3837	-
obs	-	-	92.45 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.3048	-0.0217	-0.0899	0.3142	-0.0728	0.5613	-0.0104	0.0179	-0.0168	-0.0098	0.0096	0.0275	0.0388	-0.0485	0.0008	0.0113	-0.0015	-0.0058	0.0101	-0.0048	0.0227	-0.2172	2.2997	26.0751
2	0.4861	-0.0205	-0.204	0.3111	0.0124	0.4974	0.0113	0.0083	0.0458	0.0136	0.0035	0.0214	-0.0365	-0.0214	-0.0149	0.0338	0.0009	-0.009	0.0219	-0.0004	0.0301	9.2225	20.7085	22.0685
3	0.4194	-0.068	0.2046	0.1465	-0.0028	0.2298	0.0137	-0.0128	-0.053	0.0022	0.0043	0.019	0.0479	-0.0235	-0.0181	0.0457	-0.0021	0.0052	0.0386	0.0004	0.0427	7.7886	-21.3271	70.5472
4	0.2736	0.02	0.0872	0.2866	-0.083	0.516	-0.0102	-0.0372	0.0114	0.0324	0.0098	0.0201	-0.0398	-0.0452	0.0004	0.0426	0.002	0.0048	0.0421	-0.0045	0.054	-1.6046	-2.2906	65.383
5	0.3831	0.1663	0.0324	0.4533	-0.0489	0.2903	-0.002	0.001	-0.0311	0.0004	0.0009	-0.0071	0.0262	0.006	0.001	0.0169	0.0078	-0.0029	0.0105	-0.0036	0.0088	56.4413	-25.228	77.7156
6	0.5602	0.0397	0.094	0.2576	0.0212	0.2132	0.0041	-0.047	0.0123	0.03	-0.0054	0.0292	-0.0028	-0.0242	0.0013	0.0204	0.0022	0.0027	0.0074	-0.0001	0.0041	42.1813	-14.2558	88.3125
7	0.2681	-0.0275	0.0246	0.4521	-0.1661	0.4117	0.0013	0.0124	-0.0159	-0.0197	-0.0141	-0.0429	0.0286	0.0475	0.0128	0.0067	-0.0007	0.0033	0.0136	-0.0065	0.0129	79.6354	-3.0768	38.1263
8	0.2461	0.0928	-0.0207	0.5471	-0.2605	0.3942	0.0025	-0.0243	0.0103	0.0254	-0.0203	-0.0513	-0.028	0.0574	0.0178	0.0043	-0.0009	-0.0046	0.0154	-0.0047	0.0097	79.3063	2.1877	58.8651
9	0.4723	-0.0384	-0.0523	0.2156	0.0134	0.1941	0.0052	0.0468	0.0068	-0.0314	-0.0052	0.0188	-0.0068	-0.017	0	0.0171	-0.002	-0.0012	0.0062	-0.0001	0.0036	45.0869	13.5304	6.3819
10	0.314	-0.1563	0.0402	0.423	-0.0724	0.3578	-0.0053	-0.0098	0.0217	0.0106	0.0041	-0.0195	-0.0144	0.0165	0.0012	0.0087	-0.0062	0.0034	0.0054	-0.0033	0.0049	59.457	23.8425	18.6606

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 190
2	X-RAY DIFFRACTION	2	B	1 - 194
3	X-RAY DIFFRACTION	3	C	1 - 188
4	X-RAY DIFFRACTION	4	D	1 - 193
5	X-RAY DIFFRACTION	5	E	1 - 193
6	X-RAY DIFFRACTION	6	F	1 - 194
7	X-RAY DIFFRACTION	7	G	1 - 192
8	X-RAY DIFFRACTION	8	H	1 - 193
9	X-RAY DIFFRACTION	9	I	2 - 194
10	X-RAY DIFFRACTION	10	J	1 - 191

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