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- PDB-3hhv: The crystal structure of the Thioredoxin A2 from Sulfolobus solfa... -

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Basic information

Entry
Database: PDB / ID: 3hhv
TitleThe crystal structure of the Thioredoxin A2 from Sulfolobus solfataricus
ComponentsThioredoxin (TrxA-2)
KeywordsOXIDOREDUCTASE / Protein dimeric interface / protein structure-stability / redox state / disulfide bonds / protein structure-function.
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / glycerol ether metabolic process / protein-disulfide reductase (NAD(P)H) activity / protein-disulfide reductase activity / cell redox homeostasis / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin (TrxA-2)
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsRuggiero, A. / Masullo, M. / Ruocco, M.R. / Arcari, P. / Zagari, A. / Vitagliano, L.
CitationJournal: Proteins / Year: 2009
Title: The dimeric structure of Sulfolobus solfataricus thioredoxin A2 and the basis of its thermostability
Authors: Ruggiero, A. / Masullo, M. / Marasco, D. / Ruocco, M.R. / Grimaldi, P. / Arcari, P. / Zagari, A. / Vitagliano, L.
History
DepositionMay 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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: Thioredoxin (TrxA-2)


Theoretical massNumber of molelcules
Total (without water)12,6391
Polymers12,6391
Non-polymers00
Water1,36976
1
A: Thioredoxin (TrxA-2)

A: Thioredoxin (TrxA-2)


Theoretical massNumber of molelcules
Total (without water)25,2772
Polymers25,2772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1530 Å2
ΔGint-13 kcal/mol
Surface area9360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.272, 27.882, 62.060
Angle α, β, γ (deg.)90.00, 92.34, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Thioredoxin (TrxA-2)


Mass: 12638.670 Da / Num. of mol.: 1 / Fragment: Thioredoxin A2 / Mutation: Truncated form 26-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: trxA-2, SSO2232 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97WI4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 1.93 Å3/Da / Density % sol: 36.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 18-22% PEG3350, 0.2 M ammonium iodide, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 17, 2006 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. all: 8660 / Num. obs: 8660 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 29.8
Reflection shellResolution: 1.83→1.9 Å / Rmerge(I) obs: 0.176 / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FB6

1fb6


Resolution: 1.83→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 408 -Random
Rwork0.196 ---
all0.199 8653 --
obs0.199 8653 98 %-
Refinement stepCycle: LAST / Resolution: 1.83→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms815 0 0 76 891
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.016
X-RAY DIFFRACTIONo_angle_deg1.5

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