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- PDB-3p7x: Crystal structure of an atypical two-cysteine peroxiredoxin (SAOU... -

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Basic information

Entry
Database: PDB / ID: 3p7x
TitleCrystal structure of an atypical two-cysteine peroxiredoxin (SAOUHSC_01822) from Staphylococcus aureus NCTC8325
ComponentsProbable thiol peroxidase
KeywordsOXIDOREDUCTASE / THIOREDOXIN FOLD / PEROXIDASE
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity
Similarity search - Function
Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Thiol peroxidase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsBhattacharyya, S. / Dutta, D. / Ghosh, A.K. / Das, A.K.
CitationJournal: To be Published
Title: Crystal structure of an atypical two-cysteine peroxiredoxin (SAOUHSC_01822) from Staphylococcus aureus NCTC8325
Authors: Bhattacharyya, S. / Dutta, D. / Ghosh, A.K. / Das, A.K.
History
DepositionOct 13, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable thiol peroxidase
B: Probable thiol peroxidase
C: Probable thiol peroxidase
D: Probable thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,08423
Polymers72,6704
Non-polymers3,41419
Water8,557475
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Probable thiol peroxidase
C: Probable thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,81816
Polymers36,3352
Non-polymers2,48314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-12 kcal/mol
Surface area13690 Å2
MethodPISA
3
B: Probable thiol peroxidase
D: Probable thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2667
Polymers36,3352
Non-polymers9315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-8 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.500, 149.356, 73.736
Angle α, β, γ (deg.)90.00, 104.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Probable thiol peroxidase


Mass: 18167.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: NCTC 8325 / Gene: SAOUHSC_01822, tpx / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q2FXL3, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

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Non-polymers , 5 types, 494 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 3.19 Å3/Da / Density % sol: 61.47 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0M AMMONIUM SULPHATE, 0.1M NA-HEPES PH 7, 2% (V/V) PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Jul 14, 2009 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.956→74.678 Å / Num. all: 60849 / Num. obs: 60849 / % possible obs: 92.9 % / Redundancy: 3.3 % / Rsym value: 0.047 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.96-2.062.50.4650.3412.31695568200.2730.4650.3412.271.5
2.06-2.192.80.3430.25732206977770.190.3430.2573.386.8
2.19-2.342.90.3330.25332339779480.1850.3330.2534.594.3
2.34-2.523.20.1610.1196.52496578120.0870.1610.1197.198.6
2.52-2.773.50.120.098.52571272610.0630.120.0910.199.8
2.77-3.093.70.080.05912.82457366210.0410.080.05915.2100
3.09-3.573.80.050.03619.32184557930.0260.050.03626.3100
3.57-4.373.80.0390.028241880449470.020.0390.02838.4100
4.37-6.183.80.0290.0233.61456838260.0150.0290.0241.7100
6.18-19.8453.80.0230.01640.1770120440.0120.0230.01641.996.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PSQ

1psq


Resolution: 1.96→19.85 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1897 / WRfactor Rwork: 0.1544 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8828 / SU B: 7.197 / SU ML: 0.091 / SU R Cruickshank DPI: 0.1398 / SU Rfree: 0.1325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 3072 5.1 %RANDOM
Rwork0.1683 ---
obs0.1702 60800 92.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 108.06 Å2 / Biso mean: 29.418 Å2 / Biso min: 7.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å20.55 Å2
2---1.07 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.96→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5050 0 221 475 5746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0225348
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.9887168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0785653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9125.738244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5215874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7351520
X-RAY DIFFRACTIONr_chiral_restr0.1660.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213900
X-RAY DIFFRACTIONr_mcbond_it1.0951.53252
X-RAY DIFFRACTIONr_mcangle_it1.78525236
X-RAY DIFFRACTIONr_scbond_it3.10632096
X-RAY DIFFRACTIONr_scangle_it4.854.51932
LS refinement shellResolution: 1.956→2.007 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 161 -
Rwork0.234 2907 -
all-3068 -
obs--63.48 %
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)
10.96190.4107-0.38111.5422-0.76251.5555-0.0844-0.05180.0714-0.02920.0324-0.0866-0.06260.04470.0520.03630.01120.00910.0120.00160.0318-2.31156.785112.3769
20.79430.2812-0.10262.09230.02371.28050.05530.08330.0647-0.1138-0.01130.0987-0.0747-0.089-0.0440.02320.0177-0.00120.02230.01510.0314-0.732974.1895-18.76
31.099-0.1566-0.28982.38530.57821.277-0.01530.0962-0.117-0.2453-0.06830.027-0.0202-0.14820.08360.02790.00210.00210.0224-0.01550.0149-16.261229.51615.1854
41.3110.150.05482.49131.16781.9167-0.0617-0.0772-0.07860.189-0.03070.12410.107-0.04270.09240.02620.00830.01160.011500.0139-9.319845.6314-26.8376
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 164
2X-RAY DIFFRACTION2B2 - 164
3X-RAY DIFFRACTION3C2 - 164
4X-RAY DIFFRACTION4D2 - 164

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