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- PDB-6k40: Crystal structure of alkyl hydroperoxide reductase from D. radiod... -

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Basic information

Entry
Database: PDB / ID: 6k40
TitleCrystal structure of alkyl hydroperoxide reductase from D. radiodurans R1
ComponentsAlkyl hydroperoxide reductase AhpD
KeywordsOXIDOREDUCTASE / antioxidant / hydrogen peroxide / stress resistance
Function / homology
Function and homology information


peroxiredoxin activity
Similarity search - Function
AhpD-like / Uncharacterised peroxidase-related / Alkylhydroperoxidase AhpD core / AhpD-like / AhpD-like / Carboxymuconolactone decarboxylase-like / Carboxymuconolactone decarboxylase family / AhpD-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / CMD domain-containing protein
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsKim, M.-K. / Zhang, J. / Zhao, L.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea) Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of the AhpD-like protein DR1765 from Deinococcus radiodurans R1.
Authors: Zhao, L. / Jeong, S. / Zhang, J. / Jung, J.H. / Choi, J.I. / Lim, S. / Kim, M.K.
History
DepositionMay 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 14, 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.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
G: Alkyl hydroperoxide reductase AhpD
F: Alkyl hydroperoxide reductase AhpD
H: Alkyl hydroperoxide reductase AhpD
I: Alkyl hydroperoxide reductase AhpD
J: Alkyl hydroperoxide reductase AhpD
K: Alkyl hydroperoxide reductase AhpD
L: Alkyl hydroperoxide reductase AhpD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,83929
Polymers262,18512
Non-polymers1,65417
Water25,2571402
1
A: Alkyl hydroperoxide reductase AhpD
G: Alkyl hydroperoxide reductase AhpD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0045
Polymers43,6972
Non-polymers3063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-6 kcal/mol
Surface area17710 Å2
MethodPISA
2
B: Alkyl hydroperoxide reductase AhpD
E: Alkyl hydroperoxide reductase AhpD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9885
Polymers43,6972
Non-polymers2903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-3 kcal/mol
Surface area17540 Å2
MethodPISA
3
C: Alkyl hydroperoxide reductase AhpD
D: Alkyl hydroperoxide reductase AhpD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9745
Polymers43,6972
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-7 kcal/mol
Surface area17500 Å2
MethodPISA
4
F: Alkyl hydroperoxide reductase AhpD
L: Alkyl hydroperoxide reductase AhpD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8824
Polymers43,6972
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-6 kcal/mol
Surface area17730 Å2
MethodPISA
5
H: Alkyl hydroperoxide reductase AhpD
K: Alkyl hydroperoxide reductase AhpD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8824
Polymers43,6972
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-8 kcal/mol
Surface area17660 Å2
MethodPISA
6
I: Alkyl hydroperoxide reductase AhpD
J: Alkyl hydroperoxide reductase AhpD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1106
Polymers43,6972
Non-polymers4124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-3 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.094, 166.862, 285.047
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

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Components

#1: Protein
Alkyl hydroperoxide reductase AhpD


Mass: 21848.740 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: R1 / Gene: DR_1765 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RTJ7, peroxiredoxin
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1402 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 295 K / Method: microbatch / Details: magnesium chloride, Tris-HCl, PEG 4000, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 115515 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.98 / Rmerge(I) obs: 0.514 / Net I/σ(I): 9.1
Reflection shellResolution: 2.27→2.31 Å / Rmerge(I) obs: 5.872 / Mean I/σ(I) obs: 0.889 / Num. unique obs: 5632 / CC1/2: 0.234

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OYO

2oyo


Resolution: 2.27→35.1 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1835 1.74 %
Rwork0.208 --
obs0.209 105442 91.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.87 Å2
Refinement stepCycle: LAST / Resolution: 2.27→35.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17195 0 108 1402 18705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2732-2.33470.32411110.33466178X-RAY DIFFRACTION72
2.3347-2.40340.32481330.30717217X-RAY DIFFRACTION84
2.4034-2.48090.36361260.30137352X-RAY DIFFRACTION85
2.4809-2.56960.29721280.28437455X-RAY DIFFRACTION86
2.5696-2.67240.3331400.27097575X-RAY DIFFRACTION88
2.6724-2.7940.28071330.25517841X-RAY DIFFRACTION90
2.794-2.94120.31410.24158022X-RAY DIFFRACTION92
2.9412-3.12540.23781490.22568209X-RAY DIFFRACTION94
3.1254-3.36660.23621480.21128403X-RAY DIFFRACTION96
3.3666-3.7050.21121520.18638603X-RAY DIFFRACTION98
3.705-4.24030.21081550.15958653X-RAY DIFFRACTION99
4.2403-5.33940.1811550.15188873X-RAY DIFFRACTION100
5.3394-35.1030.18251640.16269226X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 8.401 Å / Origin y: -19.6585 Å / Origin z: 36.0255 Å
111213212223313233
T0.1275 Å20.0073 Å20.0207 Å2-0.2102 Å2-0.0234 Å2--0.2294 Å2
L0.0813 °2-0.009 °20.0335 °2-0.2765 °2-0.2003 °2--0.4172 °2
S-0.0127 Å °-0.032 Å °0.0096 Å °0.0726 Å °-0.0078 Å °0.0019 Å °-0.0402 Å °-0.002 Å °0.0163 Å °
Refinement TLS groupSelection details: ALL

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