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- PDB-2v2g: Crystal Structure of the C45S mutant of the Peroxiredoxin 6 of Ar... -

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Basic information

Entry
Database: PDB / ID: 2v2g
TitleCrystal Structure of the C45S mutant of the Peroxiredoxin 6 of Arenicola Marina. Monoclinic form
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: 1.6 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 5, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 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

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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)104,08012
Polymers103,2234
Non-polymers8578
Water18,9341051
1
A: PEROXIREDOXIN 6
B: PEROXIREDOXIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0406
Polymers51,6112
Non-polymers4284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-45.4 kcal/mol
Surface area21510 Å2
MethodPQS
2
C: PEROXIREDOXIN 6
D: PEROXIREDOXIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0406
Polymers51,6112
Non-polymers4284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-49 kcal/mol
Surface area21400 Å2
MethodPQS
Unit cell
Length a, b, c (Å)127.246, 83.226, 98.349
Angle α, β, γ (deg.)90.00, 100.71, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2063-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.39612, 0.91688, 0.0493), (0.91678, 0.39195, 0.07673), (0.05103, 0.07559, -0.99583)-47.33209, 33.80177, -48.71864
2given(-0.99953, -0.0016, -0.03068), (0.00189, -0.99995, -0.00951), (-0.03067, -0.00957, 0.99948)-31.01743, 44.80171, -0.16619
3given(0.39516, -0.91841, -0.01904), (-0.91714, -0.39327, -0.06479), (0.05202, 0.04306, -0.99772)17.70544, 11.52191, -47.76283

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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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1051 / 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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 5.5
Details: RESERVOIR : BIS-TRIS 0.1M PH 5.5, PEG3350 25%(W/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: ESRF / Beamline: BM30A / Wavelength: 0.979792
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 1, 2006 / Details: TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING
RadiationMonochromator: FIRST CRYSTAL FLAT AND N2 COOLED. SECOND ONE SAGITALLY BENT
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979792 Å / Relative weight: 1
ReflectionResolution: 1.6→14 Å / Num. obs: 131708 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG

1hd2

1nm3

1prx

1qmv

1qq2

1qxh

1tp9

1we0

1x0r

1xcc

1zye

2cv4

2feg
PDB Unreleased entry


Resolution: 1.6→13.96 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.388 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 6651 5.1 %RANDOM
Rwork0.16 ---
obs0.162 125024 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.68 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→13.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6791 0 60 1051 7902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227010
X-RAY DIFFRACTIONr_bond_other_d0.0020.024895
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.9889496
X-RAY DIFFRACTIONr_angle_other_deg1.021311989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3275875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09424.139273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.508151220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.791540
X-RAY DIFFRACTIONr_chiral_restr0.1070.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027650
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021318
X-RAY DIFFRACTIONr_nbd_refined0.2160.21421
X-RAY DIFFRACTIONr_nbd_other0.2060.25182
X-RAY DIFFRACTIONr_nbtor_refined0.1770.23433
X-RAY DIFFRACTIONr_nbtor_other0.0880.23466
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2720
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.7570.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3561.55618
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56127118
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.82933056
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7854.52377
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 477
Rwork0.258 9026
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)
11.9548-0.40460.61881.55650.34891.4015-0.0556-0.14240.10950.2577-0.04450.2831-0.103-0.07880.1-0.1079-0.0060.0458-0.1577-0.0207-0.1539-15.67846.622-12.339
23.0105-1.5029-1.81963.74661.06311.7775-0.0473-0.1958-0.34890.283-0.0209-0.13640.24030.21090.0681-0.1133-0.0188-0.0119-0.12990.0321-0.12052.42421.436-17.971
31.8803-0.727-0.16481.6334-0.31641.46540.01890.1861-0.0683-0.1264-0.0648-0.06140.02310.0450.0458-0.1748-0.0187-0.0025-0.1376-0.006-0.21471.03336.764-33.701
44.4292-0.7894-1.49243.20671.54652.52390.06050.31160.1301-0.1947-0.11070.7324-0.2241-0.36320.0501-0.15220.0108-0.0397-0.0952-0.00740.0296-29.51743.202-28.741
52.2743-0.416-0.20391.44770.00211.25350.0024-0.2215-0.16420.2486-0.0656-0.02860.18330.01870.0631-0.0865-0.0319-0.0042-0.13470.0134-0.1771-15.043-1.725-12.462
63.5937-1.72482.1583.1134-1.1882.0608-0.0915-0.22860.38430.2577-0.0180.2503-0.2508-0.20030.1094-0.134-0.0270.017-0.1198-0.085-0.03-32.9423.56-18.432
71.8864-0.49820.39061.2960.28551.4910.04870.16950.0772-0.1325-0.090.10760.0502-0.03210.0413-0.1574-0.0243-0.0186-0.1251-0.033-0.1599-31.0688.365-34.266
84.8253-0.98071.40243.0502-1.39871.9481-0.00080.3519-0.0753-0.1938-0.0707-0.53090.20820.29730.0715-0.12070.01540.0417-0.1026-0.0165-0.0819-0.771.973-28.727
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 154
2X-RAY DIFFRACTION2A155 - 220
3X-RAY DIFFRACTION3B2 - 154
4X-RAY DIFFRACTION4B155 - 219
5X-RAY DIFFRACTION5C2 - 154
6X-RAY DIFFRACTION6C155 - 220
7X-RAY DIFFRACTION7D2 - 154
8X-RAY DIFFRACTION8D155 - 220

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