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- PDB-6e8l: Crystal Structure of Alkyl hydroperoxidase D (AhpD) from Streptoc... -

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Basic information

Entry
Database: PDB / ID: 6e8l
TitleCrystal Structure of Alkyl hydroperoxidase D (AhpD) from Streptococcus pneumoniae (Strain D39/ NCTC 7466)
ComponentsAlkyl hydroperoxide reductase AhpD
KeywordsOXIDOREDUCTASE / alkylhydroperoxidase peroxiredoxin
Function / homology
Function and homology information


peroxiredoxin activity
Similarity search - Function
Alkylhydroperoxidase AhpD core / AhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Carboxymuconolactone decarboxylase-like domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsMeng, Y. / Davies, J. / North, R. / Coombes, D. / Horne, C. / Hampton, M. / Dobson, R.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure-function analyses of alkylhydroperoxidase D fromStreptococcus pneumoniaereveal an unusual three-cysteine active site architecture.
Authors: Meng, Y. / Sheen, C.R. / Magon, N.J. / Hampton, M.B. / Dobson, R.C.J.
History
DepositionJul 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkyl hydroperoxide reductase AhpD
B: Alkyl hydroperoxide reductase AhpD
C: Alkyl hydroperoxide reductase AhpD
D: Alkyl hydroperoxide reductase AhpD
E: Alkyl hydroperoxide reductase AhpD
F: Alkyl hydroperoxide reductase AhpD


Theoretical massNumber of molelcules
Total (without water)119,1206
Polymers119,1206
Non-polymers00
Water4,071226
1
A: Alkyl hydroperoxide reductase AhpD
B: Alkyl hydroperoxide reductase AhpD


Theoretical massNumber of molelcules
Total (without water)39,7072
Polymers39,7072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-31 kcal/mol
Surface area15190 Å2
MethodPISA
2
C: Alkyl hydroperoxide reductase AhpD
E: Alkyl hydroperoxide reductase AhpD


Theoretical massNumber of molelcules
Total (without water)39,7072
Polymers39,7072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-31 kcal/mol
Surface area15370 Å2
MethodPISA
3
D: Alkyl hydroperoxide reductase AhpD
F: Alkyl hydroperoxide reductase AhpD


Theoretical massNumber of molelcules
Total (without water)39,7072
Polymers39,7072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-32 kcal/mol
Surface area15340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.296, 84.233, 183.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Alkyl hydroperoxide reductase AhpD


Mass: 19853.406 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
Strain: D39 / NCTC 7466 / Gene: SPD_0373 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2ZNM1, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.123806 Å3/Da / Density % sol: 42.12108 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-tris propane, 0.2 M Magnesium chloride hexahydrate, 25% w/v PEG 3350, 6% v/v 1,2-Propandiol

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953717 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953717 Å / Relative weight: 1
ReflectionResolution: 2.3→45 Å / Num. obs: 45900 / % possible obs: 99.3 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.044 / Rrim(I) all: 0.106 / Χ2: 1 / Net I/σ(I): 10.5
Reflection shellResolution: 2.44→2.54 Å / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4142 / CC1/2: 0.859 / Rpim(I) all: 0.212 / Rrim(I) all: 0.518 / Χ2: 0.91 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
Coot0.8.7model building
PHENIXrefinement
RefinementResolution: 2.3→45 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.242 --
Rwork0.196 --
obs-45900 99.3 %
Refinement stepCycle: LAST / Resolution: 2.3→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8287 0 0 226 8513

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