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- PDB-5j9c: Crystal structure of peroxiredoxin Asp f3 C31S/C61S variant -

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Basic information

Entry
Database: PDB / ID: 5j9c
TitleCrystal structure of peroxiredoxin Asp f3 C31S/C61S variant
Componentsperoxiredoxin Asp f3
KeywordsOXIDOREDUCTASE / peroxiredoxin / Aspergillus
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / IgE binding / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / cellular response to oxidative stress / protein homodimerization activity / mitochondrion / cytoplasm
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
Peroxiredoxin Asp f3
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.956 Å
AuthorsBzymek, K.P. / Williams, J.C. / Hong, T.B. / Bagramyan, K. / Kalkum, M.
CitationJournal: Sci Rep / Year: 2016
Title: The Crystal Structure of Peroxiredoxin Asp f3 Provides Mechanistic Insight into Oxidative Stress Resistance and Virulence of Aspergillus fumigatus.
Authors: Hillmann, F. / Bagramyan, K. / Straburger, M. / Heinekamp, T. / Hong, T.B. / Bzymek, K.P. / Williams, J.C. / Brakhage, A.A. / Kalkum, M.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: peroxiredoxin Asp f3
B: peroxiredoxin Asp f3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6823
Polymers38,6572
Non-polymers241
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-12 kcal/mol
Surface area14670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.860, 68.100, 90.960
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 Asp f3 / Peroxisomal membrane protein pmp20 / Thioredoxin reductase


Mass: 19328.744 Da / Num. of mol.: 2 / Mutation: C31S,C61S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: pmp20, AFUA_6G02280 / Production host: Escherichia coli (E. coli) / References: UniProt: O43099, peroxiredoxin
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 7.2, 22% PEG 3350, 0.3 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.956→30.56 Å / Num. obs: 23741 / % possible obs: 99.2 % / Redundancy: 4.2 % / CC1/2: 0.999 / Net I/σ(I): 21.7
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 4.4 / % possible all: 90.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J9B

5j9b


Resolution: 1.956→30.558 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.98
RfactorNum. reflection% reflection
Rfree0.1895 1187 5 %
Rwork0.1526 --
obs0.1545 23739 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.956→30.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 1 358 2967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082747
X-RAY DIFFRACTIONf_angle_d1.0823757
X-RAY DIFFRACTIONf_dihedral_angle_d12.393998
X-RAY DIFFRACTIONf_chiral_restr0.043408
X-RAY DIFFRACTIONf_plane_restr0.005484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.956-2.0450.26371380.17422631X-RAY DIFFRACTION94
2.045-2.15280.18831480.1572803X-RAY DIFFRACTION100
2.1528-2.28760.18671460.14912788X-RAY DIFFRACTION100
2.2876-2.46420.18011490.15772817X-RAY DIFFRACTION100
2.4642-2.7120.23171480.16292823X-RAY DIFFRACTION100
2.712-3.10410.19281490.16492833X-RAY DIFFRACTION100
3.1041-3.90960.16931510.13442866X-RAY DIFFRACTION100
3.9096-30.56160.17211580.14842991X-RAY DIFFRACTION100
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)
10.9344-0.80570.48531.41690.25931.1781-0.07030.06380.0875-0.35060.02560.131-0.0409-0.055-0.00730.08470.01540.0050.11270.01550.06598.57858.8082-15.0913
20.84180.2979-0.30770.46110.26740.56040.0876-0.01210.03050.0365-0.00120.1473-0.0550.009500.1193-0.0005-0.00340.1093-0.01090.124114.46358.7346-5.0129
31.94951.2277-0.28171.6318-0.06770.0565-0.0301-0.1960.29750.26990.08030.2602-0.02820.07640.10560.11950.01060.00520.1292-0.04020.09619.481213.93792.8345
40.40750.39440.21150.8301-0.06750.59260.0642-0.00090.1417-0.02050.04250.1294-0.0369-0.129800.1206-0.00290.01120.12020.01030.12358.35595.4333-8.0357
51.89641.8511.0252.1070.31813.74950.01390.4227-0.4169-0.21170.059-0.45550.35810.52330.54110.07230.03240.05870.1504-0.02140.094324.03443.8232-12.7661
60.69470.1546-0.11240.160.23880.69650.0298-0.09490.2739-0.01930.0085-0.1914-0.00310.015600.12240.0062-0.0020.1173-0.00050.192122.228313.9214-3.5921
75.7025-2.3788-0.75641.071.1519.3446-0.0003-0.0881.1170.01660.0927-0.4937-1.02570.40610.23390.1776-0.026-0.00580.1742-0.07940.262617.775919.56273.6703
81.86620.17370.3492.88110.61930.3178-0.06470.33930.0404-0.64950.3484-0.6113-0.04690.48750.14380.19750.02480.10010.2119-0.08460.170519.0393-28.7256-21.3772
92.0420.2853-0.04933.53080.3760.59520.1097-0.321-0.1930.6215-0.1075-0.097-0.01990.0408-0.30810.0375-0.0165-0.04730.1301-0.02530.091913.981-16.3750.3156
100.61790.2275-0.09331.09670.18391.0296-0.0047-0.1089-0.08280.12410.0346-0.02440.0358-0.005900.1142-0.0046-0.0110.1274-0.00920.120811.1012-18.5668-8.9793
110.9806-0.7898-0.01332.4631-0.17971.00550.0213-0.084-0.07470.0509-0.08980.51470.1403-0.1812-0.23920.106-0.03570.00590.1394-0.04020.1-1.1721-24.8139-9.827
120.3491-0.04380.10240.69320.58690.51220.032-0.1266-0.01460.1734-0.0332-0.01580.1782-0.007600.1337-0.0001-0.00120.1349-0.00740.10358.6864-16.3343-6.4307
131.72640.26740.93780.41810.76291.7252-0.12030.19370.1597-0.24570.01880.0031-0.27330.1637-0.30670.1077-0.00330.02870.10080.01280.085915.7199-14.8507-19.3861
141.67140.3294-0.51840.76870.50370.6818-0.07140.5173-0.1089-0.33180.0860.10570.2499-0.2071-0.03210.1458-0.02810.00180.069-0.03180.07676.7607-24.2798-21.6088
153.3827-1.74891.9351.91570.50783.37270.0565-0.0072-0.72610.03460.17940.48281.0254-0.12090.26080.2958-0.0635-0.01110.1842-0.03290.1805-1.1619-30.5014-18.2595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 80 )
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 115 )
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 135 )
6X-RAY DIFFRACTION6chain 'A' and (resid 136 through 161 )
7X-RAY DIFFRACTION7chain 'A' and (resid 162 through 169 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 15 )
9X-RAY DIFFRACTION9chain 'B' and (resid 16 through 26 )
10X-RAY DIFFRACTION10chain 'B' and (resid 27 through 65 )
11X-RAY DIFFRACTION11chain 'B' and (resid 66 through 80 )
12X-RAY DIFFRACTION12chain 'B' and (resid 81 through 110 )
13X-RAY DIFFRACTION13chain 'B' and (resid 111 through 135 )
14X-RAY DIFFRACTION14chain 'B' and (resid 136 through 161 )
15X-RAY DIFFRACTION15chain 'B' and (resid 162 through 170 )

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