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- PDB-2cx4: Crystal structure of a bacterioferritin comigratory protein perox... -

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Basic information

Entry
Database: PDB / ID: 2cx4
TitleCrystal structure of a bacterioferritin comigratory protein peroxiredoxin from the Aeropyrum pernix K1 (form-2 crystal)
Componentsbacterioferritin comigratory protein
KeywordsOXIDOREDUCTASE / antioxidant enzyme / reactive oxygen species / thioredoxin fold / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


peroxidase 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
: / Thiol peroxidase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsMizohata, E. / Murayama, K. / Idaka, M. / Tatsuguchi, A. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of a bacterioferritin comigratory protein peroxiredoxin from the Aeropyrum pernix K1 (form-2 crystal)
Authors: Mizohata, E. / Murayama, K. / Idaka, M. / Tatsuguchi, A. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 27, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bacterioferritin comigratory protein
B: bacterioferritin comigratory protein
C: bacterioferritin comigratory protein
D: bacterioferritin comigratory protein
E: bacterioferritin comigratory protein
F: bacterioferritin comigratory protein
G: bacterioferritin comigratory protein
H: bacterioferritin comigratory protein


Theoretical massNumber of molelcules
Total (without water)150,6828
Polymers150,6828
Non-polymers00
Water7,332407
1
A: bacterioferritin comigratory protein
B: bacterioferritin comigratory protein


Theoretical massNumber of molelcules
Total (without water)37,6712
Polymers37,6712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-14 kcal/mol
Surface area14320 Å2
MethodPISA
2
C: bacterioferritin comigratory protein
D: bacterioferritin comigratory protein


Theoretical massNumber of molelcules
Total (without water)37,6712
Polymers37,6712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-16 kcal/mol
Surface area14270 Å2
MethodPISA
3
E: bacterioferritin comigratory protein
F: bacterioferritin comigratory protein


Theoretical massNumber of molelcules
Total (without water)37,6712
Polymers37,6712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-14 kcal/mol
Surface area14430 Å2
MethodPISA
4
G: bacterioferritin comigratory protein
H: bacterioferritin comigratory protein


Theoretical massNumber of molelcules
Total (without water)37,6712
Polymers37,6712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-13 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.479, 132.479, 106.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
bacterioferritin comigratory protein / bacterioferritin comigratory protein peroxiredoxin


Mass: 18835.289 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: APE2125 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: GenBank: 14601861, UniProt: Q9YA14*PLUS, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 3.13 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7
Details: ammonium sulfate, MES, Tris, sodium chloride, dithiothreitol, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.96400, 0.97884, 0.97946
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 6, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9641
20.978841
30.979461
ReflectionResolution: 2.3→50 Å / Num. obs: 143980 / Biso Wilson estimate: 20 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→46.32 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: The crystal form is twinned by the operator k, h, -l, twinning fraction 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.263 --RANDOM
Rwork0.203 ---
obs0.203 143980 89.6 %-
Displacement parametersBiso mean: 49.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.3→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10328 0 0 407 10735
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.319 --
Rwork0.322 8442 -
obs--54.8 %

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