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- PDB-2v32: Crystal Structure of the C45S mutant of the Peroxiredoxin 6 of Ar... -

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Basic information

Entry
Database: PDB / ID: 2v32
TitleCrystal Structure of the C45S mutant of the Peroxiredoxin 6 of Arenicola Marina. Monoclinic form 2
ComponentsPEROXIREDOXIN 6
KeywordsOXIDOREDUCTASE / PEROXIREDOXINS / ANTIOXIDANT ENZYMES / ARENICOLA MARINA
Function / homology
Function and homology information


peroxiredoxin activity / cell redox homeostasis / mitochondrion / cytosol
Similarity search - Function
Antioxidant, Horf6; Chain A, domain 2 / Antioxidant, Horf6; Chain A, domain2 / 1-Cys peroxiredoxin / Peroxiredoxin, AhpC-type / 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 ...Antioxidant, Horf6; Chain A, domain 2 / Antioxidant, Horf6; Chain A, domain2 / 1-Cys peroxiredoxin / Peroxiredoxin, AhpC-type / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / Peroxiredoxin 6
Similarity search - Component
Biological speciesARENICOLA MARINA (lugworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSmeets, A. / Declercq, J.P.
CitationJournal: Protein Sci. / Year: 2008
Title: The Crystal Structure of the C45S Mutant of Annelid Arenicola Marina Peroxiredoxin 6 Supports its Assignment to the Mechanistically Typical 2-Cys Subfamily without Any Formation of Toroid-Shaped Decamers.
Authors: Smeets, A. / Loumaye, E. / Clippe, A. / Rees, J.F. / Knoops, B. / Declercq, J.P.
History
DepositionJun 11, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEROXIREDOXIN 6
B: PEROXIREDOXIN 6
C: PEROXIREDOXIN 6
D: PEROXIREDOXIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7118
Polymers103,2234
Non-polymers4884
Water14,484804
1
A: PEROXIREDOXIN 6
B: PEROXIREDOXIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8564
Polymers51,6112
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-47.2 kcal/mol
Surface area21620 Å2
MethodPQS
2
C: PEROXIREDOXIN 6
D: PEROXIREDOXIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8564
Polymers51,6112
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-49.3 kcal/mol
Surface area21750 Å2
MethodPQS
Unit cell
Length a, b, c (Å)128.261, 83.034, 107.444
Angle α, β, γ (deg.)90.00, 116.72, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2140-

HOH

21C-2109-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.39009, 0.92023, 0.03184), (0.92022, 0.38842, 0.04815), (0.03194, 0.04808, -0.99833)-48.12045, 33.51918, -47.85597
2given(-0.99988, 0.00476, 0.01485), (-0.00474, -0.99999, 0.00115), (0.01485, 0.00108, 0.99989)-30.85333, 45.09361, 0.36908
3given(0.39413, -0.91756, -0.05234), (-0.91853, -0.39134, -0.05621), (0.0311, 0.07023, -0.99705)16.52116, 11.52739, -48.36038

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Components

#1: Protein
PEROXIREDOXIN 6 / PEROXIREDOXIN 6 OF ARENICOLA MARINA


Mass: 25805.670 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARENICOLA MARINA (lugworm) / Plasmid: PQE-60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: Q1AN22, peroxiredoxin
#2: Chemical
ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 45 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 45 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 45 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 45 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 45 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 45 TO SER

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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: 2.48 Å3/Da / Density % sol: 50.4 % / Description: NONE
Crystal growpH: 5.5
Details: RESERVOIR : BIS-TRIS 0.1M PH 5.5, PEG3350 25%(M/V), DTT 0.001M, AMMONIUM SULFATE 0.1M DROP 1UL PROTEIN AND 1 UL RESERVOIR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 18, 2006
Details: MIRROR 1, FLAT PRE-MIRROR, MIRROR 2, BENT, VERTICALLY FOCUSSING
RadiationMonochromator: SI 111, HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 65352 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3 / % possible all: 85.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V2G

2v2g


Resolution: 2→19.83 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.876 / SU B: 5.229 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3307 5.1 %RANDOM
Rwork0.192 ---
obs0.195 62040 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.75 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6791 0 36 804 7631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226983
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.9869465
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5735873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30524.118272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.242151218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3831540
X-RAY DIFFRACTIONr_chiral_restr0.1210.21061
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025212
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.23419
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24785
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2600
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1281.54528
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69827112
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.86232833
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1414.52353
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.53 223
Rwork0.389 3721

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