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- PDB-3tco: Crystallographic and spectroscopic characterization of Sulfolobus... -

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Basic information

Entry
Database: PDB / ID: 3tco
TitleCrystallographic and spectroscopic characterization of Sulfolobus solfataricus TrxA1 provide insights into the determinants of thioredoxin fold stability
ComponentsThioredoxin (TrxA-1)
KeywordsOXIDOREDUCTASE / disulfide oxidoreductase
Function / homology
Function and homology information


protein-disulfide reductase activity / 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-1)
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEsposito, L. / Ruggiero, A. / Masullo, M. / Ruocco, M.R. / Lamberti, A. / Arcari, P. / Zagari, A. / Vitagliano, L.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Crystallographic and spectroscopic characterizations of Sulfolobus solfataricus TrxA1 provide insights into the determinants of thioredoxin fold stability.
Authors: Esposito, L. / Ruggiero, A. / Masullo, M. / Ruocco, M.R. / Lamberti, A. / Arcari, P. / Zagari, A. / Vitagliano, L.
History
DepositionAug 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Thioredoxin (TrxA-1)
B: Thioredoxin (TrxA-1)
C: Thioredoxin (TrxA-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,89511
Polymers37,3993
Non-polymers4978
Water4,197233
1
A: Thioredoxin (TrxA-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7155
Polymers12,4661
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin (TrxA-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5282
Polymers12,4661
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thioredoxin (TrxA-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6524
Polymers12,4661
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.760, 75.090, 55.350
Angle α, β, γ (deg.)90.00, 112.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thioredoxin (TrxA-1)


Mass: 12466.255 Da / Num. of mol.: 3 / Fragment: Truncated form (25-133) of Thioredoxin (TrxA-1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: trxA-1, SSO0368 / Production host: Escherichia coli (E. coli) / References: UniProt: Q980E5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% (w/v) PEG4000; 0.2 M Ammonium sulfate. Protein concentration 2-6 mg/ml., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Jan 12, 2009 / 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: 1.9→23 Å / Num. all: 28596 / Num. obs: 26928 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.2 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 93.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HHV

3hhv


Resolution: 1.9→22.48 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 273255.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1316 4.9 %RANDOM
Rwork0.189 ---
all0.19 28596 --
obs0.189 26928 87.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.3096 Å2 / ksol: 0.409449 e/Å3
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å21.72 Å2
2---1.94 Å20 Å2
3---1.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→22.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 32 233 2808
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.712
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.362.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 218 5.2 %
Rwork0.229 3945 -
obs--81.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramwater.top
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION5edo.param
X-RAY DIFFRACTION4edo.top

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