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- PDB-3qpm: Crystal structure of peroxiredoxin Prx4 from Pseudosciaena crocea -

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Basic information

Entry
Database: PDB / ID: 3qpm
TitleCrystal structure of peroxiredoxin Prx4 from Pseudosciaena crocea
ComponentsPeroxiredoxin
KeywordsOXIDOREDUCTASE / PEROXIREDOXIN / Thioredoxin fold / Peroxidase
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / endoplasmic reticulum / 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
thioredoxin-dependent peroxiredoxin
Similarity search - Component
Biological speciesLarimichthys crocea (large yellow croaker)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLian, F.M. / Teng, Y.B. / Jiang, Y.L. / He, Y.X. / Chen, Y. / Zhou, C.Z.
CitationJournal: To be Published
Title: The N-terminal beta-sheet of peroxiredoxin Prx4 in the large yellow croaker Pseudosciaena crocea is critical for its peroxidase and anti-bacterial activities
Authors: Lian, F.M. / Mu, Y.N. / Teng, Y.B. / Ao, J.Q. / Jiang, Y.L. / He, Y.X. / Chen, Y.X. / Zhou, C.Z. / Chen, X.H.
History
DepositionFeb 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin
B: Peroxiredoxin
C: Peroxiredoxin
D: Peroxiredoxin
E: Peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,44110
Polymers135,9805
Non-polymers4605
Water11,241624
1
A: Peroxiredoxin
B: Peroxiredoxin
C: Peroxiredoxin
D: Peroxiredoxin
E: Peroxiredoxin
hetero molecules

A: Peroxiredoxin
B: Peroxiredoxin
C: Peroxiredoxin
D: Peroxiredoxin
E: Peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,88120
Polymers271,96010
Non-polymers92110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area30130 Å2
ΔGint-199 kcal/mol
Surface area74480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.121, 195.998, 51.740
Angle α, β, γ (deg.)90.00, 105.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-348-

HOH

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Components

#1: Protein
Peroxiredoxin


Mass: 27196.049 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Larimichthys crocea (large yellow croaker)
Plasmid: pET28a-derived / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: H3JQV8*PLUS, peroxiredoxin
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% polyethylene glycol monomethyl ether 5000, 0.1M HEPES-NaOH, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9999 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 108135 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 5.2 / Rsym value: 0.214 / % possible all: 94.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PN8

2pn8


Resolution: 1.9→37.98 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21976 5372 5 %RANDOM
Rwork0.19561 ---
obs0.19682 102513 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.509 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å2-1.97 Å2
2---2.52 Å20 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7784 0 30 624 8438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228019
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.96410863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6165969
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30323.803355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.478151363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7891540
X-RAY DIFFRACTIONr_chiral_restr0.0930.21185
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216046
X-RAY DIFFRACTIONr_mcbond_it0.5461.54850
X-RAY DIFFRACTIONr_mcangle_it1.03727882
X-RAY DIFFRACTIONr_scbond_it1.64833169
X-RAY DIFFRACTIONr_scangle_it2.8144.52981
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 351 -
Rwork0.272 7124 -
obs--92.85 %

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