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- PDB-3tks: Crystal structure of full-length human peroxiredoxin 4 in three d... -

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Basic information

Entry
Database: PDB / ID: 3tks
TitleCrystal structure of full-length human peroxiredoxin 4 in three different redox states
Components(Peroxiredoxin-4) x 3
KeywordsOXIDOREDUCTASE / Trx fold / peroxiredoxin
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
PEROXIDE ION / Peroxiredoxin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)140,2508
Polymers140,1545
Non-polymers963
Water8,557475
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)280,50016
Polymers280,30810
Non-polymers1926
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area29080 Å2
ΔGint-177 kcal/mol
Surface area71920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.178, 140.104, 61.504
Angle α, β, γ (deg.)90.00, 102.48, 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: 28027.605 Da / Num. of mol.: 2
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: 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: 28043.604 Da / Num. of mol.: 2
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
#3: 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.: 1
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
#4: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.75 Å3/Da / Density % sol: 55.26 %
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: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 13, 2009
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 59098 / Num. obs: 57443 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0.5 / Redundancy: 3.1 % / Rmerge(I) obs: 0.085 / Χ2: 0.935 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.492.50.42555220.632194
0.71
0.761
0.7581
0.8221
0.8971
1.0131
1.1421
1.1651
1.1021

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Processing

Software
NameVersionClassificationNB
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: 2.4→30.523 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8287 / SU ML: 0.32 / σ(F): 0 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 2824 5.04 %
Rwork0.1833 --
all0.213 59098 -
obs0.1858 56068 94.82 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 108.85 Å2 / Biso mean: 39.0616 Å2 / Biso min: 13.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.6916 Å20 Å2-10.854 Å2
2---4.3822 Å2-0 Å2
3---10.5322 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7890 0 6 475 8371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088216
X-RAY DIFFRACTIONf_angle_d1.11311171
X-RAY DIFFRACTIONf_chiral_restr0.0761221
X-RAY DIFFRACTIONf_plane_restr0.0041442
X-RAY DIFFRACTIONf_dihedral_angle_d14.8353059
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 (%)
2.3996-2.48540.33482410.29674875511687
2.4854-2.58480.33213010.26385094539591
2.5848-2.70240.30172620.24665175543792
2.7024-2.84480.26572630.22565233549693
2.8448-3.02290.2452550.20435338559395
3.0229-3.2560.26882680.19815444571296
3.256-3.58320.22762940.17715469576397
3.5832-4.10070.20963080.15535514582299
4.1007-5.16230.17943130.1335533584699
5.1623-30.52580.20313190.16115569588898

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