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- PDB-4mh2: Crystal structure of Bovine Mitochondrial Peroxiredoxin III -

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Basic information

Entry
Database: PDB / ID: 4mh2
TitleCrystal structure of Bovine Mitochondrial Peroxiredoxin III
ComponentsThioredoxin-dependent peroxide reductase, mitochondrial
KeywordsOXIDOREDUCTASE / CATENANE / DODECAMER / PEROXIREDOXIN / Thioredoxin fold / mitochondrial
Function / homology
Function and homology information


Detoxification of Reactive Oxygen Species / maternal placenta development / thioredoxin-dependent peroxiredoxin / myeloid cell differentiation / thioredoxin peroxidase activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / mitochondrion organization / regulation of mitochondrial membrane potential / cell redox homeostasis / hydrogen peroxide catabolic process ...Detoxification of Reactive Oxygen Species / maternal placenta development / thioredoxin-dependent peroxiredoxin / myeloid cell differentiation / thioredoxin peroxidase activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / mitochondrion organization / regulation of mitochondrial membrane potential / cell redox homeostasis / hydrogen peroxide catabolic process / response to hydrogen peroxide / cellular response to reactive oxygen species / response to oxidative stress / response to lipopolysaccharide / early endosome / mitochondrial matrix / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Thioredoxin-dependent peroxide reductase, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCao, Z. / McGow, D.P. / Shepherd, C. / Lindsay, J.G.
CitationJournal: Plos One / Year: 2015
Title: Improved Catenated Structures of Bovine Peroxiredoxin III F190L Reveal Details of Ring-Ring Interactions and a Novel Conformational State.
Authors: Cao, Z. / McGow, D.P. / Shepherd, C. / Lindsay, J.G.
History
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Sep 9, 2020Group: Database references / Derived calculations / Structure summary
Category: struct / struct_ref_seq_dif / struct_site
Item: _struct.title / _struct_ref_seq_dif.details ..._struct.title / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin-dependent peroxide reductase, mitochondrial
B: Thioredoxin-dependent peroxide reductase, mitochondrial
C: Thioredoxin-dependent peroxide reductase, mitochondrial
D: Thioredoxin-dependent peroxide reductase, mitochondrial
E: Thioredoxin-dependent peroxide reductase, mitochondrial
F: Thioredoxin-dependent peroxide reductase, mitochondrial
G: Thioredoxin-dependent peroxide reductase, mitochondrial
H: Thioredoxin-dependent peroxide reductase, mitochondrial
I: Thioredoxin-dependent peroxide reductase, mitochondrial
J: Thioredoxin-dependent peroxide reductase, mitochondrial
K: Thioredoxin-dependent peroxide reductase, mitochondrial
L: Thioredoxin-dependent peroxide reductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,33618
Polymers292,18412
Non-polymers1,1536
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20780 Å2
ΔGint-114 kcal/mol
Surface area74580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.571, 260.825, 81.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Thioredoxin-dependent peroxide reductase, mitochondrial / Antioxidant protein 1 / AOP-1 / Peroxiredoxin-3 / Protein SP-22


Mass: 24348.629 Da / Num. of mol.: 12 / Fragment: UNP residues 63-257 / Mutation: F190L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: AOP1, PRDX3 / Plasmid: pET 14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: P35705, peroxiredoxin
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 34% 2-Methyl-1,3-Propanediol, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2008
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→258.2 Å / Num. all: 151852 / Num. obs: 149669 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 1.6 / % possible all: 96.3

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZYE

1zye


Resolution: 2.2→95.47 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.227 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21868 7516 5 %RANDOM
Rwork0.18046 ---
obs0.18235 142057 98.56 %-
all-151852 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.531 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å2-0 Å20 Å2
2--0.45 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.2→95.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15385 0 78 476 15939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01916322
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.95322253
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30552061
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21424.022741
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.836152603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.81560
X-RAY DIFFRACTIONr_chiral_restr0.1010.22503
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112514
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8242.938017
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7974.38110031
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5713.1688305
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 501 -
Rwork0.299 10042 -
obs--94.68 %
Refinement TLS params.

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

IDL11 (°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)
11.5868-0.34390.02230.7611-0.2420.7297-0.0243-0.01070.02430.03680.00850.03920.04630.05610.01590.0397-0.0254-0.00890.06510.00450.0142-2.4324-36.393812.834
21.55350.4495-0.48180.7535-0.17961.4143-0.01310.11010.0133-0.07260.0328-0.01860.0938-0.0982-0.01970.0512-0.0223-0.02160.1273-0.00090.016513.2676-31.7191-9.1719
32.15020.70580.11121.95240.23620.79660.1027-0.2149-0.14870.1371-0.0509-0.38070.03370.1158-0.05180.0149-0.0087-0.03780.14860.01260.107144.0643-19.2302-2.9305
41.49530.2027-0.14751.70960.34241.1909-0.03670.1665-0.0407-0.36420.0579-0.221-0.0547-0.0082-0.02130.0896-0.0270.05940.0935-0.02540.041650.63024.376-15.7121
51.3735-0.0945-0.10691.74520.37071.06590.0484-0.04960.1398-0.04580.058-0.3894-0.07850.2103-0.10640.0233-0.05180.03790.1297-0.04440.20659.429830.20663.9489
61.8848-0.6-0.73322.1960.8221.61360.13260.27440.0798-0.427-0.0726-0.2246-0.2284-0.0126-0.060.1406-0.03860.07160.0961-0.00380.088545.35553.79140.4497
72.09770.1027-0.6270.99650.06871.33690.0001-0.17990.05710.0720.02290.0028-0.0458-0.0102-0.0230.0839-0.0453-0.00980.062-0.02810.1227.860163.988627.3575
81.60650.2329-0.29551.6071-0.20930.88690.05160.06940.3137-0.04970.0035-0.0235-0.1286-0.033-0.05510.065-0.00520.03650.00670.00870.07870.421166.228724.3106
91.17440.5475-0.28791.429-0.11961.1402-0.0059-0.04770.08950.02310.0160.03990.04330.0567-0.01020.05040.02920.01930.0516-0.02140.0405-17.618345.957843.929
101.3606-0.0477-0.0723.53440.30920.989-0.06160.17290.1752-0.16240.01280.3940.061-0.16860.04880.0498-0.0184-0.01560.07440.01030.0756-36.78730.225631.4439
110.8233-0.113-0.07442.53620.62560.83320.0073-0.13080.02020.4500.11140.1277-0.0021-0.00730.2559-0.03280.04390.0758-0.01590.0121-33.8329-2.801736.8049
121.4189-0.66060.12981.48730.04740.81450.0099-0.0007-0.03160.13270.00590.0128-0.0415-0.0391-0.01580.0442-0.03110.01010.0513-0.01140.0113-31.3806-18.733314.5985
130.0588-0.0110.01920.08530.03360.05150.0084-00.01560.0360.0009-0.0099-0.0057-0.0035-0.00940.0966-0.01940.01140.1226-0.00560.04394.13388.999215.9666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 165
2X-RAY DIFFRACTION2B0 - 164
3X-RAY DIFFRACTION3C2 - 165
4X-RAY DIFFRACTION4D0 - 164
5X-RAY DIFFRACTION5E2 - 164
6X-RAY DIFFRACTION6F0 - 164
7X-RAY DIFFRACTION7G1 - 164
8X-RAY DIFFRACTION8H2 - 164
9X-RAY DIFFRACTION9I-1 - 163
10X-RAY DIFFRACTION10J1 - 163
11X-RAY DIFFRACTION11K1 - 164
12X-RAY DIFFRACTION12L1 - 165
13X-RAY DIFFRACTION13A301 - 377
14X-RAY DIFFRACTION13B201 - 240
15X-RAY DIFFRACTION13C201 - 227
16X-RAY DIFFRACTION13D301 - 335
17X-RAY DIFFRACTION13E201 - 227
18X-RAY DIFFRACTION13F301 - 319
19X-RAY DIFFRACTION13G201 - 242
20X-RAY DIFFRACTION13H301 - 335
21X-RAY DIFFRACTION13I201 - 257
22X-RAY DIFFRACTION13J301 - 323
23X-RAY DIFFRACTION13K201 - 228
24X-RAY DIFFRACTION13L301 - 366

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