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

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Basic information

Entry
Database: PDB / ID: 8xvw
TitleCrystal structure of N-terminal deletion mutant of Staphylococcal Thiol Peroxidase
ComponentsThiol peroxidase
KeywordsOXIDOREDUCTASE / Peroxiredoxin / Staphylococcus aureus / Anti-oxidative defense
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
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Thiol peroxidase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShukla, M. / Maji, S. / Yadav, V.K. / Das, A.K. / Bhattacharyya, S.
Funding support India, 2items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)SRG/2020/001353 India
Other governmentI/SEED/SUB/20200005 India
CitationJournal: To Be Published
Title: Crystal structure of N-terminal deletion mutant of Staphylococcal Thiol Peroxidase
Authors: Shukla, M. / Maji, S. / Yadav, V.K. / Das, A.K. / Bhattacharyya, S.
History
DepositionJan 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,57713
Polymers32,8192
Non-polymers1,75811
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-30 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.273, 72.861, 148.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 16 through 58 or resid 60 through 68 or resid 70 through 164))
d_2ens_1(chain "B" and (resid 16 through 58 or resid 60 through 68 or resid 70 through 164))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLNGLNGLYGLYAA16 - 581 - 43
d_12CYSCYSASNASNAA60 - 6845 - 53
d_13ASPASPILEILEAA70 - 16455 - 149
d_21GLNGLNGLYGLYBB16 - 581 - 43
d_22CYSCYSASNASNBB60 - 6845 - 53
d_23ASPASPILEILEBB70 - 16455 - 149

NCS oper: (Code: givenMatrix: (-0.880205829227, -0.435155896985, 0.189412363679), (-0.459413436488, 0.681124184011, -0.570095729092), (0.119067176708, -0.588820168876, -0.799445943236)Vector: 15. ...NCS oper: (Code: given
Matrix: (-0.880205829227, -0.435155896985, 0.189412363679), (-0.459413436488, 0.681124184011, -0.570095729092), (0.119067176708, -0.588820168876, -0.799445943236)
Vector: 15.1373970005, -10.5223562067, -42.1743805671)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 16409.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: tpx / Plasmid: pQE30 / Production host: Escherichia coli M15 (bacteria) / Strain (production host): M15
References: UniProt: Q2FXL3, thioredoxin-dependent peroxiredoxin

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Non-polymers , 5 types, 396 molecules

#2: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 60.99 % / Description: Orthorhombic
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG400, Ammonium Sulfate, HEPES / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→19.14 Å / Num. obs: 38875 / % possible obs: 99.08 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.57 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 27.48
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.9 % / Num. unique obs: 3585 / CC1/2: 0.884 / % possible all: 93.41

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.14 Å / SU ML: 0.1272 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.786
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1893 1945 5 %
Rwork0.1562 36926 -
obs0.1579 38871 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.54 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 110 385 2803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01972459
X-RAY DIFFRACTIONf_angle_d1.67113306
X-RAY DIFFRACTIONf_chiral_restr0.1263376
X-RAY DIFFRACTIONf_plane_restr0.013424
X-RAY DIFFRACTIONf_dihedral_angle_d11.9112364
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.757068902984 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.26121210.20082366X-RAY DIFFRACTION91.1
1.85-1.90.22751310.18512622X-RAY DIFFRACTION99.31
1.9-1.950.22961580.19012569X-RAY DIFFRACTION99.56
1.95-2.020.18641420.15862641X-RAY DIFFRACTION99.68
2.02-2.090.19431530.14272576X-RAY DIFFRACTION99.82
2.09-2.170.18531180.15632643X-RAY DIFFRACTION99.89
2.17-2.270.21111290.16742637X-RAY DIFFRACTION99.86
2.27-2.390.19011350.15462662X-RAY DIFFRACTION99.93
2.39-2.540.18621310.15542632X-RAY DIFFRACTION99.96
2.54-2.740.20421300.16162686X-RAY DIFFRACTION99.86
2.74-3.010.21251510.16822632X-RAY DIFFRACTION99.89
3.01-3.440.18031390.15072705X-RAY DIFFRACTION100
3.44-4.330.16691540.12832704X-RAY DIFFRACTION99.93
4.33-19.140.16681530.15942851X-RAY DIFFRACTION99.83
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)
11.89743750606-0.0115280874214-0.5178998654331.341716441420.1078434598312.768905832210.00617000277226-0.0694489475255-0.0038367401720.0382914558450.0125879688455-0.0293882894230.02665883915770.0391686226615-0.009977227408450.06402095435360.00234171387342-0.00569021937850.0752209909619-0.003213683700340.0761804551455-4.22919.331-14.238
21.74104558446-0.224928336024-0.6990680066782.237723077060.6517686868233.064012821580.05102850602640.116716235410.0900810973968-0.400409610321-0.00680555055461-0.216688638649-0.145565762970.181689940213-0.03545778365590.1755133937330.01232454137020.04211165478690.134055108261-0.01455226745450.1257770159587.73112.246-42.573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 16:164 OR RESID 401:407 ) )A16 - 164
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 16:164 OR RESID 401:407 ) )A401 - 407
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 16:164 OR RESID 201:202 ) )B16 - 164
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 16:164 OR RESID 201:202 ) )B201 - 202

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