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- PDB-8zxu: Crystal structure of N terminal deletion mutant of Staphylococcal... -

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Basic information

Entry
Database: PDB / ID: 8zxu
TitleCrystal structure of N terminal deletion mutant of Staphylococcal atypical two-cysteine thiol peroxidase complexed with substrate analog
ComponentsThiol peroxidase
KeywordsOXIDOREDUCTASE / Staphylococcus aureus / Virulence / Atypical two-cysteine thiol peroxidase / Mutant / Substrate analog
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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
: / 1-HYDROXYSULFANYL-4-MERCAPTO-BUTANE-2,3-DIOL / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / IMIDAZOLE / HYDROGEN PEROXIDE / Thiol peroxidase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsShukla, M. / Maji, S. / Yadav, V.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 N terminal deletion mutant of Staphylococcal atypical two-cysteine thiol peroxidase complexed with substrate analog
Authors: Shukla, M. / Maji, S. / Yadav, V.K. / Bhattacharyya, S.
History
DepositionJun 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiol peroxidase
B: Thiol peroxidase
C: Thiol peroxidase
D: Thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,95421
Polymers65,6374
Non-polymers2,31717
Water12,160675
1
A: Thiol peroxidase
D: Thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,15611
Polymers32,8192
Non-polymers1,3389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol peroxidase
hetero molecules

C: Thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,79810
Polymers32,8192
Non-polymers9798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Unit cell
Length a, b, c (Å)38.267, 148.331, 72.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Thiol peroxidase / Tpx / Peroxiredoxin tpx / Prx / Thioredoxin peroxidase / Thioredoxin-dependent peroxiredoxin


Mass: 16409.303 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: tpx, SACOL1762 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5HF61, thioredoxin-dependent peroxiredoxin

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Non-polymers , 7 types, 692 molecules

#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O2
#4: Chemical ChemComp-A1L2G / O-tert-Butylhydroxylamine


Mass: 89.136 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H11NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-DTO / 1-HYDROXYSULFANYL-4-MERCAPTO-BUTANE-2,3-DIOL


Mass: 170.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3S2
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Ammonium sulfate, HEPES, PEG400 / Temp details: Room temperature

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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: Mar 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.55→40.93 Å / Num. obs: 112790 / % possible obs: 95.7 % / Redundancy: 3.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.046 / Rrim(I) all: 0.087 / Net I/σ(I): 9 / Num. measured all: 408053
Reflection shellResolution: 1.55→1.63 Å / % possible obs: 93.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.239 / Num. measured all: 60733 / Num. unique obs: 16057 / CC1/2: 0.93 / Rpim(I) all: 0.142 / Rrim(I) all: 0.278 / Net I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PSQ

1psq


Resolution: 1.55→40.93 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.753 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19503 5635 5 %RANDOM
Rwork0.16254 ---
obs0.16419 107108 95.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.422 Å2
Baniso -1Baniso -2Baniso -3
1--7.19 Å2-0 Å2-0.05 Å2
2--3.32 Å20 Å2
3---3.88 Å2
Refinement stepCycle: 1 / Resolution: 1.55→40.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4616 0 149 675 5440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0124868
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174670
X-RAY DIFFRACTIONr_angle_refined_deg2.2911.6286568
X-RAY DIFFRACTIONr_angle_other_deg0.7791.58510757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1685608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73424.625253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7815799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8921520
X-RAY DIFFRACTIONr_chiral_restr0.1280.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.025503
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021062
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8551.5422402
X-RAY DIFFRACTIONr_mcbond_other1.8551.5412401
X-RAY DIFFRACTIONr_mcangle_it2.6662.3133002
X-RAY DIFFRACTIONr_mcangle_other2.6662.3143003
X-RAY DIFFRACTIONr_scbond_it2.1891.8362466
X-RAY DIFFRACTIONr_scbond_other2.1891.8372467
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0632.6323561
X-RAY DIFFRACTIONr_long_range_B_refined5.72731.27721128
X-RAY DIFFRACTIONr_long_range_B_other5.56430.58820452
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A45350.12
12B45350.12
21A45310.11
22C45310.11
31A44960.12
32D44960.12
41B44650.13
42C44650.13
51B45520.11
52D45520.11
61C45170.11
62D45170.11
LS refinement shellResolution: 1.55→1.588 Å
RfactorNum. reflection% reflection
Rfree0.283 390 -
Rwork0.227 7624 -
obs--91.3 %
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)
10.10640.1258-0.00370.47530.15530.11250.01750.00780.0074-0.0028-0.0175-0.0057-0.0105-0.01610.00010.00560.0003-0.00130.01190.00520.034813.8688-14.628819.2924
20.1353-0.10020.02760.3440.14870.11950.0139-0.0054-0.00490.0077-0.01350.00140.0127-0.0118-0.00040.00450.00220.00320.01230.00510.0324-5.607613.941517.4361
30.01210.07350.00810.5428-0.14310.5493-0.0018-0.0031-0.00960.0055-0.0052-0.0397-0.08340.01670.0070.0167-0.0073-0.00050.01480.01690.034917.3197-31.867748.7786
40.02360.10370.08450.60580.17620.59690.0132-0.01310.00930.0253-0.04270.02260.0861-0.04860.02950.0158-0.01190.0040.0189-0.01640.03092.1076-42.551712.4464
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 601
2X-RAY DIFFRACTION2B16 - 901
3X-RAY DIFFRACTION3C16 - 201
4X-RAY DIFFRACTION4D16 - 501

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