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- PDB-3drn: The crystal structure of Bcp1 from Sulfolobus Sulfataricus -

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Basic information

Entry
Database: PDB / ID: 3drn
TitleThe crystal structure of Bcp1 from Sulfolobus Sulfataricus
ComponentsPeroxiredoxin, bacterioferritin comigratory protein homolog
KeywordsOXIDOREDUCTASE / Peroxiredoxin / Bacterioferritin comigratory protein
Function / homology
Function and homology information


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
CITRIC ACID / Peroxiredoxin, bacterioferritin comigratory protein homolog (Bcp-1)
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsD'Ambrosio, K. / De Simone, G.
CitationJournal: Proteins / Year: 2009
Title: Insights into the catalytic mechanism of the Bcp family: functional and structural analysis of Bcp1 from Sulfolobus solfataricus
Authors: D'Ambrosio, K. / Limauro, D. / Pedone, E. / Galdi, I. / Pedone, C. / Bartolucci, S. / De Simone, G.
History
DepositionJul 11, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxiredoxin, bacterioferritin comigratory protein homolog
B: Peroxiredoxin, bacterioferritin comigratory protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6236
Polymers37,0542
Non-polymers5684
Water4,161231
1
A: Peroxiredoxin, bacterioferritin comigratory protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7192
Polymers18,5271
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peroxiredoxin, bacterioferritin comigratory protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9034
Polymers18,5271
Non-polymers3763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.841, 91.829, 52.542
Angle α, β, γ (deg.)90.00, 95.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peroxiredoxin, bacterioferritin comigratory protein homolog / / Bcp-1 / Bacterioferritin comigratory protein 1


Mass: 18527.162 Da / Num. of mol.: 2 / Mutation: C45S, C50S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: bcp-1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus (DE3)-RIL / References: UniProt: Q97WP9, peroxiredoxin
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.25M ammonium acetate, 24% PEG 4000, 0.1M Sodium citrate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.99985 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 2, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 21792 / % possible obs: 98 %
Reflection shellResolution: 2.15→2.22 Å / % possible all: 82.2

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A4V

2a4v


Resolution: 2.15→20 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1040 4.7 %RANDOM
Rwork0.189 20362 --
all-21792 --
obs-21402 96 %-
Solvent computationBsol: 53.425 Å2
Displacement parametersBiso max: 72.58 Å2 / Biso mean: 31.957 Å2 / Biso min: 15.05 Å2
Baniso -1Baniso -2Baniso -3
1--3.012 Å20 Å24.016 Å2
2---1.35 Å20 Å2
3---4.362 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 38 231 2701
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2971.5
X-RAY DIFFRACTIONc_scbond_it2.2532
X-RAY DIFFRACTIONc_mcangle_it1.9622
X-RAY DIFFRACTIONc_scangle_it3.222.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4cit.param
X-RAY DIFFRACTION5gol.param

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