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- PDB-2v41: Crystal Structure of the C45S mutant of the Peroxiredoxin 6 of Ar... -

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Basic information

Entry
Database: PDB / ID: 2v41
TitleCrystal Structure of the C45S mutant of the Peroxiredoxin 6 of Arenicola Marina. Orthorhombic form
ComponentsPEROXIREDOXIN 6.
KeywordsOXIDOREDUCTASE / ANTIOXIDANT ENZYMES / PEROXIREDOXINS / ARENICOLA MARINA
Function / homology
Function and homology information


peroxiredoxin activity
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: 2.4 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 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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

Downloads & links

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Assembly

Deposited unit
A: PEROXIREDOXIN 6.
B: PEROXIREDOXIN 6.
C: PEROXIREDOXIN 6.
D: PEROXIREDOXIN 6.
E: PEROXIREDOXIN 6.
F: PEROXIREDOXIN 6.
G: PEROXIREDOXIN 6.
H: PEROXIREDOXIN 6.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,42216
Polymers206,4458
Non-polymers9778
Water5,296294
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 area5470 Å2
ΔGint-46.4 kcal/mol
Surface area21990 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 area5340 Å2
ΔGint-49 kcal/mol
Surface area21860 Å2
MethodPQS
3
E: PEROXIREDOXIN 6.
F: 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 area5590 Å2
ΔGint-40.1 kcal/mol
Surface area21310 Å2
MethodPQS
4
G: PEROXIREDOXIN 6.
H: 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 area5650 Å2
ΔGint-43.9 kcal/mol
Surface area21050 Å2
MethodPQS
Unit cell
Length a, b, c (Å)77.110, 111.156, 229.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99068, -0.13544, 0.01483), (-0.13602, 0.97693, -0.16462), (0.00781, -0.1651, -0.98625)-68.10345, -8.42543, -45.6694
2given(-0.91939, -0.09065, 0.38276), (0.10738, -0.99396, 0.02251), (0.37841, 0.0618, 0.92357)-20.29872, -1.92073, 3.83645
3given(0.93161, -0.01884, -0.36296), (0.03985, -0.98734, 0.15352), (-0.36126, -0.15749, -0.91907)26.03214, -1.076, -63.76045
4given(0.99386, 0.06432, -0.09001), (-0.08481, -0.07955, -0.99322), (-0.07105, 0.99475, -0.07361)16.11838, -83.97467, -33.13151
5given(-0.99584, -0.04424, 0.07966), (0.07507, 0.0973, 0.99242), (-0.05166, 0.99427, -0.09358)-48.56987, -32.5609, -32.92659
6given(0.98202, 0.18874, -0.0035), (-0.01938, 0.08239, -0.99641), (-0.18777, 0.97857, 0.08457)14.37058, -27.86139, -81.3776
7given(-0.99741, 0.07166, -0.00624), (0.01103, 0.23807, 0.97119), (0.07108, 0.9686, -0.23824)-54.12822, 18.85763, -80.03432

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Components

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


Mass: 25805.670 Da / Num. of mol.: 8 / 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 / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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 ENGINEERED RESIDUE IN CHAIN E, CYS 45 TO SER ENGINEERED RESIDUE IN CHAIN F, CYS 45 TO SER ENGINEERED RESIDUE IN CHAIN G, CYS 45 TO SER ENGINEERED RESIDUE IN CHAIN H, 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: 2.37 Å3/Da / Density % sol: 48.11 % / Description: NONE
Crystal growpH: 5.5
Details: RESERVOIR : BIS TRIS 0.1 M PH 5.5 , PEG 3350 25%(W/V). DTT 0.001 M 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: 2.4→15 Å / Num. obs: 77362 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.2
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.3 / % possible all: 96.9

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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: 2.4→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 17.534 / SU ML: 0.199 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3823 5 %RANDOM
Rwork0.177 ---
obs0.18 72061 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13593 0 72 294 13959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02213976
X-RAY DIFFRACTIONr_bond_other_d0.0020.029741
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.98618941
X-RAY DIFFRACTIONr_angle_other_deg1.033323860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79151748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23124.107543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.645152441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6221580
X-RAY DIFFRACTIONr_chiral_restr0.0970.22124
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022637
X-RAY DIFFRACTIONr_nbd_refined0.2050.22694
X-RAY DIFFRACTIONr_nbd_other0.2010.29800
X-RAY DIFFRACTIONr_nbtor_refined0.1760.26566
X-RAY DIFFRACTIONr_nbtor_other0.0890.27156
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2390
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8021.511230
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.051214237
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.86336087
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6074.54704
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: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 204
Rwork0.232 3748
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)
12.1720.20380.41432.50030.26851.9841-0.01280.33310.2295-0.44910.001-0.2585-0.22310.30040.0119-0.1192-0.04440.056-0.18410.0318-0.1385-24.591116.3532-32.211
29.02220.2671.6174.05790.27482.92250.07530.5826-0.2134-0.5939-0.18120.43730.1716-0.37270.106-0.0663-0.0529-0.1009-0.1096-0.0434-0.0177-54.69442.687-34.2732
32.93790.02490.23481.86860.4252.467-0.0356-0.16390.20110.0446-0.01870.3406-0.2351-0.38820.0542-0.17210.00050.0099-0.2091-0.0193-0.1267-46.482116.2011-16.8411
48.8161-0.0728-0.65383.7081-0.38042.7236-0.05-0.7724-0.03810.39270.0226-0.52770.18570.70020.0274-0.09260.0256-0.0549-0.0685-0.0123-0.0258-14.79577.3386-12.559
52.1789-0.51160.00621.6762-0.02563.0314-0.0075-0.0188-0.21230.13670.05920.19530.2866-0.5048-0.0517-0.1274-0.0995-0.0215-0.17790.0063-0.1699-11.5321-21.5171-34.1161
64.759-0.417-0.81143.4958-0.69732.98020.02730.58890.2643-0.2074-0.3748-0.6816-0.51060.90010.3475-0.0408-0.0906-0.05530.13290.12050.032317.5479-11.7624-48.1734
73.0583-0.0164-0.85651.9368-0.56032.6904-0.0865-0.0999-0.09370.24770.0293-0.38910.18740.42390.0573-0.099-0.0017-0.1176-0.1927-0.0126-0.09814.5347-23.1433-27.936
810.36370.9074-4.18974.17150.27115.968-0.2089-0.89180.48380.83610.18470.2190.0168-0.33950.02420.12360.0663-0.0085-0.0203-0.0047-0.1217-12.5368-11.2163-12.7256
92.6477-0.57841.60843.12790.93645.5372-0.34540.19570.2626-0.16450.2082-0.3742-1.15761.04350.13720.0639-0.27-0.0241-0.03350.0254-0.1459-4.3389-51.2442-12.7221
104.5965-1.49240.39642.9026-0.41957.577-0.11550.12260.7435-0.3616-0.11680.5748-1.6063-1.16310.23230.4560.2784-0.30890.1471-0.14620.3002-34.8398-45.4041-24.1245
112.89930.02120.86053.33640.74483.869-0.0833-0.2655-0.14170.0403-0.19710.63260.0118-0.85430.2804-0.1647-0.0558-0.0091-0.0401-0.0476-0.0607-27.392-64.7487-12.3565
128.7795-0.19620.7052.56211.00399.6194-0.17020.2372-1.0576-0.26020.4286-0.73850.90322.2691-0.2584-0.00740.04620.12850.6501-0.17360.08913.0923-70.4322-24.3048
132.4398-0.1426-0.84033.0453-0.99173.47750.0125-0.04540.18650.0745-0.177-0.3321-0.30630.26330.1646-0.1667-0.0675-0.0217-0.13510.0529-0.186-6.50726.0515-63.4497
145.73711.4708-0.83261.7907-0.5946.2482-0.0920.38221.1803-0.40070.54751.1979-0.6715-1.124-0.45550.00490.0217-0.1370.59320.31620.3991-38.79857.5555-71.5693
152.4142-0.0092-0.57242.6273-0.80152.8491-0.11320.1931-0.1131-0.24450.24050.47730.35-0.7721-0.1273-0.1688-0.1561-0.04010.08080.0334-0.1545-28.249-8.7833-58.2794
169.30941.2868-0.63644.4729-1.0235.106-0.4461-0.0068-1.1811-0.7225-0.2695-0.8941.25450.32390.71560.28910.13920.2778-0.00280.12710.08710.7731-14.4181-73.0491
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 169
2X-RAY DIFFRACTION2A170 - 221
3X-RAY DIFFRACTION3B2 - 169
4X-RAY DIFFRACTION4B170 - 221
5X-RAY DIFFRACTION5C2 - 169
6X-RAY DIFFRACTION6C170 - 217
7X-RAY DIFFRACTION7D2 - 169
8X-RAY DIFFRACTION8D170 - 221
9X-RAY DIFFRACTION9E2 - 169
10X-RAY DIFFRACTION10E170 - 221
11X-RAY DIFFRACTION11F2 - 169
12X-RAY DIFFRACTION12F170 - 221
13X-RAY DIFFRACTION13G2 - 169
14X-RAY DIFFRACTION14G170 - 221
15X-RAY DIFFRACTION15H2 - 169
16X-RAY DIFFRACTION16H170 - 221

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