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- PDB-4rqx: Crystal structure of human peroxiredoxin 4(THIOREDOXIN PEROXIDASE... -

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Basic information

Entry
Database: PDB / ID: 4rqx
TitleCrystal structure of human peroxiredoxin 4(THIOREDOXIN PEROXIDASE) with MESNA
ComponentsPeroxiredoxin-4
KeywordsOXIDOREDUCTASE / PEROXIREDOXIN / THIOREDOXIN
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
1-THIOETHANESULFONIC ACID / Peroxiredoxin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.256 Å
AuthorsBadger, J. / Sridhar, V. / Logan, C. / Hausheer, F.H. / Nienaber, V.L.
CitationJournal: Molecules / Year: 2015
Title: Cysteine Specific Targeting of the Functionally Distinct Peroxiredoxin and Glutaredoxin Proteins by the Investigational Disulfide BNP7787.
Authors: Parker, A.R. / Petluru, P.N. / Nienaber, V.L. / Badger, J. / Leverett, B.D. / Jair, K. / Sridhar, V. / Logan, C. / Ayala, P.Y. / Kochat, H. / Hausheer, F.H.
History
DepositionNov 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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.details / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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)127,99510
Polymers127,2845
Non-polymers7115
Water3,441191
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)255,99020
Polymers254,56810
Non-polymers1,42210
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area17870 Å2
ΔGint-154 kcal/mol
Surface area65660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.004, 139.684, 96.191
Angle α, β, γ (deg.)90.00, 103.17, 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: 25456.846 Da / Num. of mol.: 5 / Fragment: UNP residues 79-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q13162, peroxiredoxin
#2: Chemical
ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O3S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE MESNA MOLECULES (RESIDUE COM) WHICH ARE VERY FLEXIBLE, ARE POORLY ORDERED IN THE STRUCTURE. THE ...THE MESNA MOLECULES (RESIDUE COM) WHICH ARE VERY FLEXIBLE, ARE POORLY ORDERED IN THE STRUCTURE. THE AUTHORS KNOW FROM MASS SPECTROSCOPY DATA THAT 1-2 MESNA MOLECULES ARE ATTACHED PER PROTEIN CHAIN. MOREOVER, AS MESNA IS COVALENT ATTACHED TO THE PROTEIN PRIOR TO CRYSTALLIZATION, MESNA MUST BE PRESENT AT THE SAME SITE IN ALL MOLECULES. SINCE MESNA IS FAIRLY CLEARLY EVIDENT IN COPY-A IT MUST BE PRESENT IN OTHER PROTEIN COPIES EVEN IF THE DENSITY IS VERY WEAK AT SOME SITES

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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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M ammonium sulfate, 0.1 M MES, 10% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.256→50 Å / Num. obs: 62860 / % possible obs: 97.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13
Reflection shellResolution: 2.256→2.35 Å / Redundancy: 3 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5856 / % possible all: 92.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PN8

2pn8


Resolution: 2.256→33.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.879 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24951 3168 5.1 %RANDOM
Rwork0.20812 ---
obs0.2102 59375 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.294 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.01 Å2
2--0.04 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.256→33.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6566 0 35 191 6792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226811
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9679275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0535825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40123.488324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.064151058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2931545
X-RAY DIFFRACTIONr_chiral_restr0.0920.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215209
X-RAY DIFFRACTIONr_mcbond_it1.05424115
X-RAY DIFFRACTIONr_mcangle_it1.8882.56673
X-RAY DIFFRACTIONr_scbond_it232696
X-RAY DIFFRACTIONr_scangle_it3.0814.52602
LS refinement shellResolution: 2.256→2.314 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.374 170
Rwork0.357 2998

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