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- PDB-3tkp: Crystal structure of full-length human peroxiredoxin 4 in the red... -

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Basic information

Entry
Database: PDB / ID: 3tkp
TitleCrystal structure of full-length human peroxiredoxin 4 in the reduced form
ComponentsPeroxiredoxin-4
KeywordsOXIDOREDUCTASE / Thioredoxin fold / peroxiredoxin
Function / homology
Function and homology information


: / negative regulation of male germ cell proliferation / I-kappaB phosphorylation / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / molecular sequestering activity / extracellular matrix organization / cell redox homeostasis / hydrogen peroxide catabolic process / male gonad development ...: / negative regulation of male germ cell proliferation / I-kappaB phosphorylation / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / molecular sequestering activity / extracellular matrix organization / cell redox homeostasis / hydrogen peroxide catabolic process / male gonad development / secretory granule lumen / spermatogenesis / molecular adaptor activity / response to oxidative stress / 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: 2.49 Å
AuthorsWang, X. / Wang, L. / Wang, X. / Sun, F. / Wang, C.-C.
CitationJournal: Biochem.J. / Year: 2011
Title: Structural insights into the peroxidase activity and inactivation of human peroxiredoxin 4
Authors: Wang, X. / Wang, L. / Wang, X. / Sun, F. / Wang, C.-C.
History
DepositionAug 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 1, 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)140,0585
Polymers140,0585
Non-polymers00
Water5,585310
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)280,11610
Polymers280,11610
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area28100 Å2
ΔGint-183 kcal/mol
Surface area72340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.149, 141.120, 61.295
Angle α, β, γ (deg.)90.00, 103.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 28011.605 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX4 / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q13162, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.75 Å3/Da / Density % sol: 55.34 % / Mosaicity: 0.462 °
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.8M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 5mM DTT, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9998 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. all: 52910 / Num. obs: 52328 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 2.5 % / Biso Wilson estimate: 40.46 Å2 / Rmerge(I) obs: 0.054 / Χ2: 0.738 / Net I/σ(I): 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.49-2.592.40.32.552550.44399.8
2.59-2.692.40.23953070.45199.8
2.69-2.822.50.19152220.46899.7
2.82-2.962.50.13452310.52299.5
2.96-3.152.50.09652230.60299.4
3.15-3.392.50.06752740.69599.1
3.39-3.732.50.04852230.83699
3.73-4.272.50.03952480.98598.8
4.27-5.382.50.03351851.07398.1
5.38-502.50.03551601.395.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PN8

2pn8


Resolution: 2.49→45.12 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.8453 / SU ML: 0.35 / σ(F): 0 / Phase error: 22.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 2665 5.1 %Random
Rwork0.1799 ---
all0.215 52910 --
obs0.182 52304 98.16 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 90.43 Å2 / Biso mean: 41.5513 Å2 / Biso min: 19.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.8772 Å20 Å2-13.0261 Å2
2--3.2613 Å2-0 Å2
3---10.6083 Å2
Refinement stepCycle: LAST / Resolution: 2.49→45.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7874 0 0 310 8184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088102
X-RAY DIFFRACTIONf_angle_d1.15111003
X-RAY DIFFRACTIONf_chiral_restr0.081206
X-RAY DIFFRACTIONf_plane_restr0.0051412
X-RAY DIFFRACTIONf_dihedral_angle_d13.9292986
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4863-2.57520.27062800.22954670495093
2.5752-2.67830.28482500.219850585308100
2.6783-2.80010.27312790.210449825261100
2.8001-2.94770.26982640.20385023528799
2.9477-3.13240.25912870.20164972525999
3.1324-3.37420.24012810.19355001528299
3.3742-3.71360.24052700.18984995526599
3.7136-4.25060.20712730.16545005527899
4.2506-5.35390.16782480.13794978522698
5.3539-45.12530.18592330.17464955518896

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