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- PDB-9kzm: Crystal structure of C36S mutant Glutathione peroxidase of Staphy... -

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Basic information

Entry
Database: PDB / ID: 9kzm
TitleCrystal structure of C36S mutant Glutathione peroxidase of Staphylococcus aureus.
ComponentsGlutathione peroxidase homolog BsaA
KeywordsOXIDOREDUCTASE / Glutathione peroxidase / Active site mutant / ROS defense / Staphylococcus aureus / Virulence
Function / homologyGlutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / peroxidase activity / cellular response to oxidative stress / Thioredoxin-like superfamily / Glutathione peroxidase homolog BsaA
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMaji, S. / Shukla, M. / Yadav, V.K. / Jena, A.K. / Bhattacharyya, S.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)SRG/2020/001353 India
CitationJournal: To Be Published
Title: Crystal structure of C36S mutant Glutathione peroxidase of Staphylococcus aureus.
Authors: Maji, S. / Shukla, M. / Yadav, V.K. / Jena, A.K. / Bhattacharyya, S.
History
DepositionDec 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione peroxidase homolog BsaA


Theoretical massNumber of molelcules
Total (without water)18,1241
Polymers18,1241
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.795, 95.921, 59.786
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-242-

HOH

21A-417-

HOH

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Components

#1: Protein Glutathione peroxidase homolog BsaA


Mass: 18123.604 Da / Num. of mol.: 1 / Mutation: C36S
Source method: isolated from a genetically manipulated source
Details: C36S mutant / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: bsaA, SACOL1325 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HGC7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97893 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.5→47.96 Å / Num. obs: 29292 / % possible obs: 100 % / Redundancy: 14.2 % / Biso Wilson estimate: 17.57 Å2 / CC1/2: 1 / Net I/σ(I): 25.6
Reflection shellResolution: 1.5→1.58 Å / Num. unique obs: 4198 / CC1/2: 0.937

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→39.47 Å / SU ML: 0.1375 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9151
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1668 1476 5.05 %
Rwork0.1493 27768 -
obs0.1503 29244 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.12 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 0 218 1497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01131320
X-RAY DIFFRACTIONf_angle_d1.19411779
X-RAY DIFFRACTIONf_chiral_restr0.0694184
X-RAY DIFFRACTIONf_plane_restr0.0126233
X-RAY DIFFRACTIONf_dihedral_angle_d6.0521172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.27811330.24042478X-RAY DIFFRACTION99.5
1.55-1.60.28381220.21842475X-RAY DIFFRACTION99.73
1.6-1.670.25131450.19092496X-RAY DIFFRACTION99.92
1.67-1.740.20171380.17672496X-RAY DIFFRACTION99.77
1.74-1.840.19931280.16272511X-RAY DIFFRACTION100
1.84-1.950.18691250.15072496X-RAY DIFFRACTION99.85
1.95-2.10.16361420.152520X-RAY DIFFRACTION99.92
2.1-2.310.17381000.1382558X-RAY DIFFRACTION99.96
2.31-2.650.15921390.14792535X-RAY DIFFRACTION99.96
2.65-3.330.16591370.14612564X-RAY DIFFRACTION100
3.34-39.470.13671670.1322639X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 10.021954206 Å / Origin y: 16.8147611357 Å / Origin z: 4.04567237303 Å
111213212223313233
T0.118562454492 Å2-0.0032209921036 Å20.0153141812715 Å2-0.140254314697 Å2-0.00860754675081 Å2--0.114494180622 Å2
L3.4343924472 °2-0.599837641293 °20.142463147925 °2-1.65602909334 °2-0.409348746073 °2--1.43592773851 °2
S0.000711759096365 Å °0.0875094157411 Å °-0.140748726498 Å °-0.0297324074224 Å °-0.0103822022134 Å °-0.0155953885264 Å °0.0637963052343 Å °0.0178712228927 Å °0.00937026212978 Å °
Refinement TLS groupSelection details: all

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