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- PDB-3hjp: The crystal structure of Bcp4 from Sulfolobus Solfataricus -

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Basic information

Entry
Database: PDB / ID: 3hjp
TitleThe crystal structure of Bcp4 from Sulfolobus Solfataricus
ComponentsPeroxiredoxin, bacterioferritin comigratory protein homolog (Bcp-4)
KeywordsOXIDOREDUCTASE / Peroxiredoxin / Bacterioferritin comigratory protein
Function / homology
Function and homology information


antioxidant activity / oxidoreductase activity
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
Peroxiredoxin, bacterioferritin comigratory protein homolog (Bcp-4)
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsD'Ambrosio, K. / De Simone, G.
CitationJournal: To be Published
Title: Exploring the catalytic mechanism of the first dimeric Bcp: functional, structural and docking analysis
Authors: Limauro, D. / D'Ambrosio, K. / Pedone, E. / Langella, E. / Galdi, I. / Pedone, C. / De Simone, G. / Bartolucci, S.
History
DepositionMay 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin, bacterioferritin comigratory protein homolog (Bcp-4)
B: Peroxiredoxin, bacterioferritin comigratory protein homolog (Bcp-4)
C: Peroxiredoxin, bacterioferritin comigratory protein homolog (Bcp-4)
D: Peroxiredoxin, bacterioferritin comigratory protein homolog (Bcp-4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2358
Polymers74,0934
Non-polymers1424
Water3,711206
1
A: Peroxiredoxin, bacterioferritin comigratory protein homolog (Bcp-4)
B: Peroxiredoxin, bacterioferritin comigratory protein homolog (Bcp-4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1174
Polymers37,0472
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-37 kcal/mol
Surface area13690 Å2
MethodPISA
2
C: Peroxiredoxin, bacterioferritin comigratory protein homolog (Bcp-4)
D: Peroxiredoxin, bacterioferritin comigratory protein homolog (Bcp-4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1174
Polymers37,0472
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-37 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.227, 64.142, 76.692
Angle α, β, γ (deg.)90.00, 114.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peroxiredoxin, bacterioferritin comigratory protein homolog (Bcp-4) / / Bcp4 / bacterioferritin comigratory protein 4


Mass: 18523.279 Da / Num. of mol.: 4 / Mutation: C45S, C50S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: bcp4 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q97VL0, peroxiredoxin
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: 0.15 M ammonium acetate, 25% PEG 4000, 0.1 M Sodium acetate , pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 4, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 20646 / % possible obs: 96.1 % / Redundancy: 3.6 % / Rsym value: 0.055 / Net I/σ(I): 20
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.333 / % possible all: 77.4

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DRN

3drn


Resolution: 2.55→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 962 -RANDOM
Rwork0.204 ---
obs0.204 19734 91.8 %-
all-20646 --
Solvent computationBsol: 39.245 Å2
Displacement parametersBiso max: 98.67 Å2 / Biso mean: 47.45 Å2 / Biso min: 17.93 Å2
Baniso -1Baniso -2Baniso -3
1-8.221 Å20 Å2-0.536 Å2
2---8.35 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4984 0 4 206 5194
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_mcbond_it1.2811.5
X-RAY DIFFRACTIONc_scbond_it1.9452
X-RAY DIFFRACTIONc_mcangle_it2.1852
X-RAY DIFFRACTIONc_scangle_it2.9932.5
LS refinement shellResolution: 2.55→2.6 Å /
RfactorNum. reflection
Rfree0.371 32
Rwork0.376 -

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