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- PDB-2wfc: Crystal structure of peroxiredoxin 5 from Arenicola Marina -

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Basic information

Entry
Database: PDB / ID: 2wfc
TitleCrystal structure of peroxiredoxin 5 from Arenicola Marina
ComponentsPEROXIREDOXIN 5
KeywordsOXIDOREDUCTASE / ANTIOXIDANT ENZYMES
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / cellular response to oxidative stress / mitochondrion
Similarity search - Function
Peroxiredoxin-5-like / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Peroxiredoxin-5
Similarity search - Component
Biological speciesARENICOLA MARINA (lugworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSmeets, A. / Declercq, J.P.
CitationJournal: To be Published
Title: Crystal Structure of Peroxiredoxin 5 from Arenicola Marina
Authors: Smeets, A. / Knoops, B. / Declercq, J.P.
History
DepositionApr 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEROXIREDOXIN 5
B: PEROXIREDOXIN 5
C: PEROXIREDOXIN 5
D: PEROXIREDOXIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1235
Polymers70,0644
Non-polymers591
Water11,295627
1
A: PEROXIREDOXIN 5
D: PEROXIREDOXIN 5


Theoretical massNumber of molelcules
Total (without water)35,0322
Polymers35,0322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-11.8 kcal/mol
Surface area12670 Å2
MethodPISA
2
B: PEROXIREDOXIN 5
C: PEROXIREDOXIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0913
Polymers35,0322
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-12.6 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.210, 112.070, 68.910
Angle α, β, γ (deg.)90.00, 97.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.70006, 0.67805, -0.22397), (-0.6789, -0.72922, -0.08563), (-0.22138, 0.0921, 0.97083)-27.85693, 133.74178, 17.19934
2given(0.39762, -0.89875, 0.18477), (-0.90257, -0.41935, -0.09751), (0.16512, -0.128, -0.97793)37.60585, 120.47395, 31.58232
3given(0.23292, 0.95799, 0.16736), (0.95858, -0.25517, 0.12653), (0.16392, 0.13096, -0.97774)-40.09594, 51.82991, -0.88668

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Components

#1: Protein
PEROXIREDOXIN 5 / PRDX5


Mass: 17516.062 Da / Num. of mol.: 4 / Fragment: RESIDUES 28-186 / 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: Q1AN23, peroxiredoxin
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 74 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 74 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 74 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 74 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 74 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 74 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: 1.98 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growDetails: PEG 4000 29%(W/V), DTT 0.001 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
DetectorType: ADSC CCD / Detector: CCD / Details: SECOND CRYSTAL SAGITALLY BENT
RadiationMonochromator: FIRST CRYSTAL FLAT AND N2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.75→34.17 Å / Num. obs: 51140 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.7
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.4 / % possible all: 82.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HD2

1hd2


Resolution: 1.75→68.36 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.654 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2596 5.1 %RANDOM
Rwork0.163 ---
obs0.165 48544 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20.43 Å2
2--1.1 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.75→68.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4620 0 4 627 5251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224707
X-RAY DIFFRACTIONr_bond_other_d0.0010.023108
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9746375
X-RAY DIFFRACTIONr_angle_other_deg0.9637696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4035632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73926.098164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20315776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.358158
X-RAY DIFFRACTIONr_chiral_restr0.1030.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215276
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02828
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8831.53143
X-RAY DIFFRACTIONr_mcbond_other0.3011.51316
X-RAY DIFFRACTIONr_mcangle_it1.43825014
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.52931564
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7734.51361
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: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 172 -
Rwork0.227 3070 -
obs--82.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6440.462-0.38152.2946-0.1323.09580.0184-0.0366-0.08710.1452-0.02850.0388-0.0005-0.02940.010.0095-0.00170.00130.00170.00460.046814.8154.7420.063
21.8697-0.3886-0.4431.93970.0833.22190.006-0.20070.05070.2135-0.00310.0173-0.00560.0383-0.00290.0292-0.0069-0.00480.0231-0.00470.02-5.77582.02638.384
31.68010.4184-0.27911.87720.01653.8685-0.02110.19250.0488-0.0902-0.0044-0.0499-0.0499-0.07780.02540.0058-0.00150.00090.03080.0050.0196-1.85181.9337.217
43.03030.7164-1.98161.8558-0.42125.1356-0.21230.7022-0.1856-0.34990.08950.03420.228-0.7060.12280.0821-0.0484-0.01440.2135-0.0710.068219.3354.689-11.043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 187
2X-RAY DIFFRACTION2B29 - 187
3X-RAY DIFFRACTION3C29 - 187
4X-RAY DIFFRACTION3C1188
5X-RAY DIFFRACTION4D29 - 187

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