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- PDB-3tjg: Crystal Structure of human peroxiredoxin IV C51A mutant in oxidiz... -

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Basic information

Entry
Database: PDB / ID: 3tjg
TitleCrystal Structure of human peroxiredoxin IV C51A mutant in oxidized 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: 2.24 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)144,0175
Polymers144,0175
Non-polymers00
Water13,313739
1
A: Peroxiredoxin-4
B: Peroxiredoxin-4
C: Peroxiredoxin-4
D: Peroxiredoxin-4
E: Peroxiredoxin-4

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


Theoretical massNumber of molelcules
Total (without water)288,03410
Polymers288,03410
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area18370 Å2
ΔGint-136 kcal/mol
Surface area68500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.160, 139.070, 95.140
Angle α, β, γ (deg.)90.00, 102.29, 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) / References: UniProt: Q13162, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 739 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 48% PEG200, 0.1 M Tris, pH 7.0, 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: 2.24→28.96 Å / Num. all: 64808 / Num. obs: 64808 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.5
Reflection shellResolution: 2.24→2.3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4733 / % possible all: 99.8

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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: 2.24→28.96 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 10.99 / SU ML: 0.119 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.183 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20111 3285 5.1 %RANDOM
Rwork0.15778 ---
all0.15997 64807 --
obs0.15997 61522 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.929 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å20 Å2-2.84 Å2
2--0.16 Å20 Å2
3----4.06 Å2
Refinement stepCycle: LAST / Resolution: 2.24→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6787 0 0 739 7526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227283
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9679934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365917
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22823.427356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85151265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4031557
X-RAY DIFFRACTIONr_chiral_restr0.1140.21091
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215638
X-RAY DIFFRACTIONr_mcbond_it0.8861.54355
X-RAY DIFFRACTIONr_mcangle_it1.57627127
X-RAY DIFFRACTIONr_scbond_it2.46932928
X-RAY DIFFRACTIONr_scangle_it3.8374.52781
LS refinement shellResolution: 2.24→2.302 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 223 -
Rwork0.272 4484 -
obs-4733 100 %
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)
13.2327-0.56071.85581.2959-0.45062.9969-0.26060.07210.34880.1291-0.0502-0.0987-0.43310.22340.31080.0876-0.0640.00180.15850.02150.201614.03294.14449.4268
21.5658-0.990.27323.68960.12912.9313-0.0766-0.07240.03210.62720.01350.04940.0908-0.30770.06310.1402-0.05090.02850.1057-0.03310.019410.9852-9.388232.7178
31.7296-0.90510.24275.13190.33151.5369-0.1270.01390.03110.5029-0.0076-0.6304-0.07960.29960.13460.1147-0.0395-0.06410.06730.03550.108728.8611-38.916332.8449
41.15060.27430.06632.25610.85054.1390.1264-0.04460.02620.4838-0.0231-0.00910.1119-0.1495-0.10330.16410.0410.0220.07340.04760.038512.6748-60.544734.9521
51.62210.52390.69871.77811.0734.13530.12570.1463-0.27840.18920.0554-0.2160.47720.1111-0.18120.09030.07220.01820.1815-0.00090.197912.2002-78.77636.4436
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A77 - 243
2X-RAY DIFFRACTION2B77 - 246
3X-RAY DIFFRACTION3C77 - 246
4X-RAY DIFFRACTION4D77 - 245
5X-RAY DIFFRACTION5E76 - 242

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