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- PDB-6q5v: 1-Cys SiPrx, a Prx6-family 1-Cys peroxiredoxin of the thermoacido... -

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Basic information

Entry
Database: PDB / ID: 6q5v
Title1-Cys SiPrx, a Prx6-family 1-Cys peroxiredoxin of the thermoacidophilic archaeon Sulfolobus islandicus
ComponentsPeroxiredoxin
KeywordsOXIDOREDUCTASE / Archaea / Peroxiredoxin / Sulfolobus islandicus
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / peroxidase activity / cytoplasm
Similarity search - Function
Antioxidant, Horf6; Chain A, domain 2 / Antioxidant, Horf6; Chain A, domain2 / Peroxiredoxin, TDXH subfamily / 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 / Peroxiredoxin, TDXH subfamily / 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
Biological speciesSulfolobus islandicus (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.747 Å
AuthorsStroobants, S. / Maes, D. / Peeters, E. / van Molle, I.
Funding support Belgium, 1items
OrganizationGrant numberCountry
AO-2004-070 Belgium
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Structure of the Prx6-subfamily 1-Cys peroxiredoxin from Sulfolobus islandicus.
Authors: Stroobants, S. / Van Molle, I. / Saidi, Q. / Jonckheere, K. / Maes, D. / Peeters, E.
History
DepositionDec 9, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionMay 29, 2019ID: 6GWW
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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
F: Peroxiredoxin
G: Peroxiredoxin
H: Peroxiredoxin
I: Peroxiredoxin
J: Peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)246,76710
Polymers246,76710
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38850 Å2
ΔGint-302 kcal/mol
Surface area69830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.789, 159.060, 189.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Peroxiredoxin


Mass: 24676.654 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus (strain REY15A) (acidophilic)
Strain: REY15A / Gene: SiRe_0346 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CondonPlus / References: UniProt: F0NEA3, peroxiredoxin

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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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% w/v PEG1500 and 0.1M MgCl2 in a 10 mMTris buffer

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.747→76.186 Å / Num. obs: 51577 / % possible obs: 74.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 64.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.044 / Rrim(I) all: 0.105 / Net I/σ(I): 12.7
Reflection shellResolution: 2.747→2.862 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 33 / Num. unique obs: 2580 / CC1/2: 0.776 / Rpim(I) all: 0.433 / Rrim(I) all: 1.053 / % possible all: 33

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3a2v

3a2v


Resolution: 2.747→76.186 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.25
Details: The diffraction data is anisotropic so STARANISO was used for an anisotrpic resolution cut-off and scaling. The determined cut-offs for the a*, b* and c* axes are 3.65 , 2.76 and 2.55 A ...Details: The diffraction data is anisotropic so STARANISO was used for an anisotrpic resolution cut-off and scaling. The determined cut-offs for the a*, b* and c* axes are 3.65 , 2.76 and 2.55 A respectively. Based on this information we choose a resolution cut-off at 2.75 A. As a result of this procedure, the overall completeness and the completeness in the highest resolution shell are low. However, the completeness is >95% in all shells up to a resolution of 3.4 A.
RfactorNum. reflection% reflection
Rfree0.2282 2631 5.11 %
Rwork0.213 --
obs0.2137 51522 74.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.747→76.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16820 0 0 0 16820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117280
X-RAY DIFFRACTIONf_angle_d1.60323470
X-RAY DIFFRACTIONf_dihedral_angle_d26.41510340
X-RAY DIFFRACTIONf_chiral_restr0.0692600
X-RAY DIFFRACTIONf_plane_restr0.0082950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7468-2.79680.4176660.40131063X-RAY DIFFRACTION31
2.7968-2.85060.4501620.36711158X-RAY DIFFRACTION34
2.8506-2.90880.447500.36481250X-RAY DIFFRACTION36
2.9088-2.9720.3539770.36951370X-RAY DIFFRACTION40
2.972-3.04120.4796790.34961490X-RAY DIFFRACTION44
3.0412-3.11720.4423810.3621716X-RAY DIFFRACTION49
3.1172-3.20150.34741270.34311875X-RAY DIFFRACTION56
3.2015-3.29570.31511170.33062167X-RAY DIFFRACTION64
3.2957-3.40210.33511600.30162619X-RAY DIFFRACTION77
3.4021-3.52370.30331460.26853036X-RAY DIFFRACTION88
3.5237-3.66480.24661600.25443244X-RAY DIFFRACTION94
3.6648-3.83150.2731930.24993400X-RAY DIFFRACTION99
3.8315-4.03350.25561910.23343443X-RAY DIFFRACTION100
4.0335-4.28620.20542010.18743435X-RAY DIFFRACTION100
4.2862-4.61710.18111960.16483455X-RAY DIFFRACTION100
4.6171-5.08170.15081690.1583492X-RAY DIFFRACTION100
5.0817-5.81680.20511870.16613495X-RAY DIFFRACTION100
5.8168-7.32760.19191650.17643551X-RAY DIFFRACTION100
7.3276-76.21510.16742040.17193632X-RAY DIFFRACTION99
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)
10.16010.18580.09641.49860.7182.68560.0897-0.12880.021-0.1702-0.07370.1258-0.1028-0.23090.00240.26890.11750.00580.46350.02290.4022-10.0105110.8923-8.132
20.29170.1410.07761.65530.61732.41420.0339-0.07210.0126-0.26180.1112-0.3036-0.14440.07190.21450.35180.05370.12710.40320.00450.39986.6614109.325-15.7189
30.6904-0.43280.02542.5529-0.68621.10410.07010.009-0.0621-0.0862-0.05820.11840.096-0.3013-0.06160.160.0083-0.01180.3505-0.02850.3105-9.232490.416938.5485
40.59610.09470.13231.3373-1.01151.97060.02840.0401-0.012-0.0256-0.0367-0.16080.0886-0.00050.10960.16790.0480.00490.2695-0.04170.3846.748398.227533.9624
50.6337-0.188-0.39361.72560.92421.7830.04610.06320.0828-0.1267-0.09680.146-0.0044-0.05580.02530.2916-0.0325-0.05180.26470.04270.3427-6.121839.843633.9552
60.8397-0.4603-0.02582.49580.84540.76320.10420.05160.1362-0.1775-0.1654-0.20940.03560.0821-0.26790.2957-0.05480.01990.37480.07080.37919.907547.412238.8864
70.6184-0.1837-0.2511.2037-0.94382.2780.1384-0.0190.0223-0.13420.02890.14680.2695-0.1310.21860.818-0.0048-0.02280.3643-0.03480.3748-5.677528.3825-15.6331
80.8243-0.0791-0.29081.2925-0.81962.51920.1782-0.05160.0633-0.1639-0.0576-0.08190.18330.21530.22450.61380.04150.06270.3905-0.00770.36810.882326.5962-7.8092
90.313-0.1283-0.58982.37440.74321.80460.12140.00770.019-0.1051-0.11410.1907-0.1457-0.28580.08720.2480.0701-0.0710.36630.03330.4049-7.357272.4899-41.795
100.1288-0.08-0.82422.74290.38732.20320.067-0.0934-0.05-0.00250.08980.0374-0.03850.44520.29260.22910.02350.03680.4139-0.0270.30439.358865.0651-41.2843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 5:212)
2X-RAY DIFFRACTION2(chain B and resseq 5:212)
3X-RAY DIFFRACTION3(chain C and resseq 5:212)
4X-RAY DIFFRACTION4(chain D and resseq 5:212)
5X-RAY DIFFRACTION5(chain E and resseq 5:212)
6X-RAY DIFFRACTION6(chain F and resseq 5:212)
7X-RAY DIFFRACTION7(chain G and resseq 5:212)
8X-RAY DIFFRACTION8(chain H and resseq 5:212)
9X-RAY DIFFRACTION9(chain I and resseq 5:212)
10X-RAY DIFFRACTION10(chain J and resseq 5:212)

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