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- PDB-5enu: Crystal structure of an alkyl hyroperoxide reductase from Burkhol... -

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Basic information

Entry
Database: PDB / ID: 5enu
TitleCrystal structure of an alkyl hyroperoxide reductase from Burkholderia ambifaria
ComponentsAlkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen
KeywordsOXIDOREDUCTASE / SSGCID / Peroxiredoxin / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / cellular response to oxidative stress / cytoplasm
Similarity search - Function
: / Peroxiredoxin, AhpC-type / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
thioredoxin-dependent peroxiredoxin
Similarity search - Component
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of an alkyl hyroperoxide reductase from Burkholderia ambifaria
Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionNov 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen
B: Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen


Theoretical massNumber of molelcules
Total (without water)36,0612
Polymers36,0612
Non-polymers00
Water6,990388
1
A: Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen


Theoretical massNumber of molelcules
Total (without water)18,0311
Polymers18,0311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen


Theoretical massNumber of molelcules
Total (without water)18,0311
Polymers18,0311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.340, 37.010, 75.360
Angle α, β, γ (deg.)90.000, 110.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen


Mass: 18030.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: MC40-6 / Gene: BamMC406_1774 / Plasmid: BuamA.01056.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1YRI5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 1.94 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MORPHEUS B4: 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 100mM MES/imidazole pH6.5, 30mM NaF, 30mM NaBr, 30mM, NaI; BuamA.01056.a.B1.PS02485 at 17mg/mL; Direct cryo; tray 266491b4; puck gry8-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 23, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 61179 / Num. obs: 60081 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4.34 % / Biso Wilson estimate: 11.08 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.056 / Χ2: 1.008 / Net I/σ(I): 17.24 / Num. measured all: 260972
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.35-1.393.60.7960.4313.0215808452543830.50696.9
1.39-1.420.8640.3623.8916789437442190.41896.5
1.42-1.460.9220.2915.2518569422541370.3397.9
1.46-1.510.9530.2336.518505416140730.26497.9
1.51-1.560.9720.1738.4617704401239080.19797.4
1.56-1.610.9790.14310.1717212389938060.16397.6
1.61-1.670.9850.11811.916561373636810.13498.5
1.67-1.740.9890.113.7515927357835320.11398.7
1.74-1.820.9920.0816.6415349348634320.09198.5
1.82-1.910.9940.06719.6114516332932780.07698.5
1.91-2.010.9960.05423.3113568311430820.06199
2.01-2.130.9970.04726.4212960302529900.05498.8
2.13-2.280.9970.04329.0512206282128010.04999.3
2.28-2.460.9980.0430.6911317263126110.04699.2
2.46-2.70.9980.03932.6310473241623970.04499.2
2.7-3.020.9980.03534.29602219921880.03999.5
3.02-3.490.9990.03136.718441192219170.03599.7
3.49-4.270.9990.02937.727227167016620.03399.5
4.27-6.040.9990.02938.075518130912900.03298.5
6.040.9980.0336.127207476940.03492.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIX(dev_2210)refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
ARPmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ixrA

Resolution: 1.35→50 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1708 1979 3.29 %Random selection
Rwork0.1345 58087 --
obs0.1357 60066 98.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.38 Å2 / Biso mean: 17.2265 Å2 / Biso min: 5.88 Å2
Refinement stepCycle: final / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 0 0 389 2771
Biso mean---29.06 -
Num. residues----310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072599
X-RAY DIFFRACTIONf_angle_d0.8963546
X-RAY DIFFRACTIONf_chiral_restr0.087397
X-RAY DIFFRACTIONf_plane_restr0.007469
X-RAY DIFFRACTIONf_dihedral_angle_d21.498997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.38380.24851410.20654089X-RAY DIFFRACTION97
1.3838-1.42120.19941410.16484027X-RAY DIFFRACTION97
1.4212-1.4630.21441400.13894073X-RAY DIFFRACTION98
1.463-1.51030.17321360.12864132X-RAY DIFFRACTION98
1.5103-1.56420.17571410.12444085X-RAY DIFFRACTION98
1.5642-1.62690.16781360.12014126X-RAY DIFFRACTION98
1.6269-1.70090.16681420.12114106X-RAY DIFFRACTION98
1.7009-1.79060.16711440.12894152X-RAY DIFFRACTION98
1.7906-1.90270.20481400.13264159X-RAY DIFFRACTION99
1.9027-2.04960.17091450.13124189X-RAY DIFFRACTION99
2.0496-2.25580.16171400.12914160X-RAY DIFFRACTION99
2.2558-2.58220.17681430.13644223X-RAY DIFFRACTION99
2.5822-3.25280.18451400.13764260X-RAY DIFFRACTION100
3.2528-500.1371500.13334306X-RAY DIFFRACTION98

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