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- PDB-4af2: C61S mutant of thiol peroxidase form E. coli. -

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Basic information

Entry
Database: PDB / ID: 4af2
TitleC61S mutant of thiol peroxidase form E. coli.
ComponentsTHIOL PEROXIDASE
KeywordsOXIDOREDUCTASE / INACTIVE MUTANT / PEROXIREDOXIN
Function / homology
Function and homology information


hydroperoxide reductase activity / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cellular response to oxidative stress / periplasmic space / cytosol
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
Thiol peroxidase / Thiol peroxidase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBeckham, K.S.H. / Roe, A.J. / Byron, O. / Gabrielsen, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: The Structure of an Orthorhombic Crystal Form of a `Forced Reduced' Thiol Peroxidase Reveals Lattice Formation Aided by the Presence of the Affinity Tag
Authors: Beckham, K.S.H. / Byron, O. / Roe, A.J. / Gabrielsen, M.
History
DepositionJan 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOL PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)21,6221
Polymers21,6221
Non-polymers00
Water4,035224
1
A: THIOL PEROXIDASE

A: THIOL PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)43,2452
Polymers43,2452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1440 Å2
ΔGint-9.4 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.370, 71.750, 121.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein THIOL PEROXIDASE / SCAVENGASE P20


Mass: 21622.414 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: TUV / Plasmid: PET-151 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A864, UniProt: P0A862*PLUS, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 61 TO SER

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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: 3.09 Å3/Da / Density % sol: 60.16 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M MGCL2, 0.1 M TRIS PH 7, 10% POLYETHYLENE GLYCOL 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.97→40.97 Å / Num. obs: 15679 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 24.53 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.5
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HVV

3hvv


Resolution: 1.97→18.01 Å / Cor.coef. Fo:Fc: 0.9198 / Cor.coef. Fo:Fc free: 0.8681 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.205 / SU Rfree Blow DPI: 0.185 / SU Rfree Cruickshank DPI: 0.175
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 782 5 %RANDOM
Rwork0.2293 ---
obs0.2318 15636 99.8 %-
Displacement parametersBiso mean: 38.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.8351 Å20 Å20 Å2
2---1.4374 Å20 Å2
3---0.6023 Å2
Refinement stepCycle: LAST / Resolution: 1.97→18.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 0 224 1529
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091338HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.171824HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d452SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes195HARMONIC5
X-RAY DIFFRACTIONt_it1338HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion18.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion189SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1704SEMIHARMONIC4
LS refinement shellResolution: 1.97→2.11 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.238 126 4.51 %
Rwork0.2113 2665 -
all0.2124 2791 -
obs--99.8 %
Refinement TLS params.Method: refined / Origin x: -9.8679 Å / Origin y: -10.6057 Å / Origin z: 11.791 Å
111213212223313233
T-0.215 Å20.0136 Å20.0079 Å2--0.2567 Å20.0625 Å2--0.3702 Å2
L2.2881 °2-0.5015 °2-0.1379 °2-2.29 °20.44 °2--0.7236 °2
S-0.0669 Å °-0.4192 Å °-0.2997 Å °0.4262 Å °0.0401 Å °0.0851 Å °0.1269 Å °0.057 Å °0.0267 Å °
Refinement TLS groupSelection details: CHAIN A

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