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- PDB-3tjb: Crystal structure of wild-type human peroxiredoxin IV -

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Basic information

Entry
Database: PDB / ID: 3tjb
TitleCrystal structure of wild-type human peroxiredoxin IV
ComponentsPeroxiredoxin-4
KeywordsOXIDOREDUCTASE / thioredoxin fold / sulfenylation / endoplasmic reticulum
Function / homology
Function and homology information


cellular response to stress / negative regulation of male germ cell proliferation / I-kappaB phosphorylation / thioredoxin-dependent peroxiredoxin / molecular sequestering activity / thioredoxin peroxidase activity / protein maturation by protein folding / extracellular matrix organization / cell redox homeostasis / hydrogen peroxide catabolic process ...cellular response to stress / negative regulation of male germ cell proliferation / I-kappaB phosphorylation / thioredoxin-dependent peroxiredoxin / molecular sequestering activity / thioredoxin peroxidase activity / protein maturation by protein folding / extracellular matrix organization / cell redox homeostasis / hydrogen peroxide catabolic process / male gonad development / spermatogenesis / secretory granule lumen / ficolin-1-rich granule lumen / response to oxidative stress / molecular adaptor activity / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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

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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)144,1775
Polymers144,1775
Non-polymers00
Water14,052780
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)288,35510
Polymers288,35510
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area17470 Å2
ΔGint-127 kcal/mol
Surface area69270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.980, 139.430, 95.920
Angle α, β, γ (deg.)90.00, 102.81, 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: 28835.494 Da / Num. of mol.: 5 / Fragment: UNP residues 38-271
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / 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: 49.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.1 M HEPES, pH 7.3, 11% PEG8000, 8% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2010 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.37→69.71 Å / Num. all: 55077 / Num. obs: 55077 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 9.6
Reflection shellResolution: 2.37→2.44 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4093 / % possible all: 99

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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: 2.38→69.71 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.943 / SU B: 15.87 / SU ML: 0.16 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.246 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22095 2719 5.1 %RANDOM
Rwork0.16275 ---
all0.16563 53768 --
obs0.16563 51049 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.119 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å2-1.33 Å2
2--1.61 Å20 Å2
3----3.73 Å2
Refinement stepCycle: LAST / Resolution: 2.38→69.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6774 0 0 780 7554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227113
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9689675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4475879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73423.392339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.416151228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5861552
X-RAY DIFFRACTIONr_chiral_restr0.1080.21074
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215437
X-RAY DIFFRACTIONr_mcbond_it0.8081.54262
X-RAY DIFFRACTIONr_mcangle_it1.48826950
X-RAY DIFFRACTIONr_scbond_it2.32432851
X-RAY DIFFRACTIONr_scangle_it3.8124.52710
LS refinement shellResolution: 2.38→2.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 194 -
Rwork0.288 3861 -
obs-4093 98.21 %
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)
13.4652-0.48641.3591.1308-0.29132.5056-0.1098-0.15870.230.0634-0.0286-0.0573-0.26760.15530.13840.0428-0.0552-0.00780.13270.00740.133714.34883.94919.6593
21.6611-1.0750.25793.1696-0.13562.0878-0.0524-0.0102-0.01370.53530.00070.10450.0898-0.18230.05170.1336-0.04890.03110.0982-0.01740.0111.2637-9.759533.0238
31.3507-0.8447-0.2214.2140.63181.3034-0.10960.0143-0.06170.33060.042-0.4298-0.00610.24370.06760.1586-0.0144-0.02780.04940.01910.084128.7688-38.499233.2046
41.02270.093-0.30341.9651.14573.81820.1021-0.0330.03190.3178-0.016-0.0223-0.0639-0.1003-0.0860.18930.02690.02120.06480.05650.053712.681-60.360334.9925
51.60890.14680.28941.51960.62024.2990.02030.1513-0.2490.14670.0148-0.09570.3708-0.0129-0.03510.05330.04450.00610.15180.01140.163112.3565-78.7986.3251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A76 - 245
2X-RAY DIFFRACTION2B76 - 242
3X-RAY DIFFRACTION3C76 - 242
4X-RAY DIFFRACTION4D76 - 245
5X-RAY DIFFRACTION5E76 - 242

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