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- PDB-3tjf: Crystal Structure of human peroxiredoxin IV C51A mutant in reduce... -

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Basic information

Entry
Database: PDB / ID: 3tjf
TitleCrystal Structure of human peroxiredoxin IV C51A mutant in reduced form
ComponentsPeroxiredoxin-4
KeywordsOXIDOREDUCTASE / thioredoxin fold / sulfenylation / endoplasmic reticulum
Function / homology
Function and homology information


I-kappaB phosphorylation / negative regulation of male germ cell proliferation / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / molecular sequestering activity / extracellular matrix organization / cell redox homeostasis / protein maturation / hydrogen peroxide catabolic process / male gonad development ...I-kappaB phosphorylation / negative regulation of male germ cell proliferation / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / molecular sequestering activity / extracellular matrix organization / cell redox homeostasis / protein maturation / hydrogen peroxide catabolic process / male gonad development / response to oxidative stress / secretory granule lumen / spermatogenesis / molecular adaptor activity / ficolin-1-rich granule lumen / Neutrophil degranulation / endoplasmic reticulum / extracellular exosome / extracellular region / identical protein binding / nucleus / 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 ...: / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsCao, Z. / Tavender, T.J. / Roszak, A.W. / Cogdell, R.J. / Bulleid, N.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of Reduced and of Oxidized Peroxiredoxin IV Enzyme Reveals a Stable Oxidized Decamer and a Non-disulfide-bonded Intermediate in the Catalytic Cycle.
Authors: Cao, Z. / Tavender, T.J. / Roszak, A.W. / Cogdell, R.J. / Bulleid, N.J.
History
DepositionAug 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin-4
B: Peroxiredoxin-4
C: Peroxiredoxin-4
D: Peroxiredoxin-4
E: Peroxiredoxin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,45820
Polymers144,0175
Non-polymers1,44115
Water14,304794
1
A: Peroxiredoxin-4
B: Peroxiredoxin-4
C: Peroxiredoxin-4
D: Peroxiredoxin-4
E: Peroxiredoxin-4
hetero molecules

A: Peroxiredoxin-4
B: Peroxiredoxin-4
C: Peroxiredoxin-4
D: Peroxiredoxin-4
E: Peroxiredoxin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,91640
Polymers288,03410
Non-polymers2,88230
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area36110 Å2
ΔGint-648 kcal/mol
Surface area71050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.348, 138.849, 96.236
Angle α, β, γ (deg.)90.00, 103.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Peroxiredoxin-4 / Peroxiredoxin IV / Antioxidant enzyme AOE372 / AOE37-2 / Prx-IV / Thioredoxin peroxidase AO372 / ...Peroxiredoxin IV / Antioxidant enzyme AOE372 / AOE37-2 / Prx-IV / Thioredoxin peroxidase AO372 / Thioredoxin-dependent peroxide reductase A0372


Mass: 28803.428 Da / Num. of mol.: 5 / Fragment: UNP residues 38-271 / Mutation: C51A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX4 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13162, peroxiredoxin
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.55 M ammonium sulfate, 12% glycerol, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2010 / Details: MIRRORS
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.04→28.97 Å / Num. all: 87136 / Num. obs: 87136 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.3
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 4 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6233 / % possible all: 96.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0110refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PN8

2pn8


Resolution: 2.04→28.77 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 8.208 / SU ML: 0.098 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.19711 4344 5 %RANDOM
Rwork0.15965 ---
all0.16152 87117 --
obs0.16152 82773 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.144 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å2-0.85 Å2
2---0.17 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 2.04→28.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7819 0 75 794 8688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228331
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.97611367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08951034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85323.955397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.202151406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4211550
X-RAY DIFFRACTIONr_chiral_restr0.1070.21227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216390
X-RAY DIFFRACTIONr_mcbond_it0.7691.54969
X-RAY DIFFRACTIONr_mcangle_it1.39328106
X-RAY DIFFRACTIONr_scbond_it2.24933362
X-RAY DIFFRACTIONr_scangle_it3.5464.53231
LS refinement shellResolution: 2.04→2.092 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 275 -
Rwork0.276 5926 -
obs-6233 96.29 %
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)
11.2639-0.29091.00710.9535-0.43811.9533-0.05170.07340.16490.0224-0.0166-0.0727-0.1610.11760.06840.0312-0.04080.00410.0678-0.00450.067316.21452.379412.2093
20.8589-0.39490.27681.817-0.35451.3976-0.0109-0.1356-0.00490.16950.00670.104-0.0363-0.10660.00430.0714-0.02660.01680.085-0.04040.03139.3411-6.929131.1809
30.2379-0.11560.13243.35720.21520.5831-0.0138-0.04550.03550.03730.0247-0.4007-0.01740.17-0.0110.03850.0067-0.00870.09860.01370.096528.4771-42.603633.0025
40.50940.33660.13651.64310.48971.4745-0.0076-0.09-0.02440.1722-0.03220.0648-0.0175-0.05950.03980.10890.04570.01760.11050.05460.03512.5346-57.811836.803
50.78140.1460.75780.76380.22212.40430.0060.0236-0.19960.00470.0287-0.0610.27610.1828-0.03470.06490.05260.03950.06250.00950.104410.7473-79.57893.1388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 269
2X-RAY DIFFRACTION2B75 - 269
3X-RAY DIFFRACTION3C74 - 269
4X-RAY DIFFRACTION4D75 - 268
5X-RAY DIFFRACTION5E73 - 268

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