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- PDB-2fa4: Crystal Structure of Oxidized Form from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 2fa4
TitleCrystal Structure of Oxidized Form from Saccharomyces cerevisiae
ComponentsThioredoxin II
KeywordsELECTRON TRANSPORT / ALPHA/BETA SANDWICH / DIMER
Function / homology
Function and homology information


membrane fusion priming complex / protein deglutathionylation / TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / vacuole inheritance / The NLRP3 inflammasome / vacuole fusion, non-autophagic / sulfate assimilation / disulfide oxidoreductase activity / Detoxification of Reactive Oxygen Species ...membrane fusion priming complex / protein deglutathionylation / TP53 Regulates Metabolic Genes / Interconversion of nucleotide di- and triphosphates / vacuole inheritance / The NLRP3 inflammasome / vacuole fusion, non-autophagic / sulfate assimilation / disulfide oxidoreductase activity / Detoxification of Reactive Oxygen Species / fungal-type vacuole / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / deoxyribonucleotide biosynthetic process / Oxidative Stress Induced Senescence / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / glutathione metabolic process / cell redox homeostasis / protein transport / Golgi membrane / nucleus / cytoplasm / cytosol
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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsBao, R. / Tang, Y.J. / Zhou, C.Z. / Chen, Y.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of the yeast cytoplasmic thioredoxin Trx2
Authors: Bao, R. / Chen, Y. / Tang, Y.J. / Janin, J. / Zhou, C.Z.
History
DepositionDec 6, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin II
B: Thioredoxin II


Theoretical massNumber of molelcules
Total (without water)24,3482
Polymers24,3482
Non-polymers00
Water1,54986
1
A: Thioredoxin II


Theoretical massNumber of molelcules
Total (without water)12,1741
Polymers12,1741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin II


Theoretical massNumber of molelcules
Total (without water)12,1741
Polymers12,1741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.151, 83.151, 64.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MET / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 1 - 104 / Label seq-ID: 8 - 111

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Thioredoxin II / TR-II / Thioredoxin 1


Mass: 12173.913 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P22803
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 4.6
Details: 0.2M ammonium sulfate, 0.1M sodium acetate buffer, 30%(w/v) PEG mmE 2000, pH 4.6, EVAPORATION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 30, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.376→30.165 Å / Num. all: 9601 / Num. obs: 9445 / % possible obs: 98.3 % / Observed criterion σ(F): 10.5 / Observed criterion σ(I): 110.5
Reflection shellHighest resolution: 2.4 Å / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→30.16 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.895 / SU B: 5.769 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.418 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25861 453 4.8 %RANDOM
Rwork0.20583 ---
obs0.20818 8991 98.29 %-
all-9601 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.943 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.38→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 0 86 1656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221600
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9652168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.15206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.3392660
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31315274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.717152
X-RAY DIFFRACTIONr_chiral_restr0.1070.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021180
X-RAY DIFFRACTIONr_nbd_refined0.2250.2702
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21108
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0760.24
X-RAY DIFFRACTIONr_mcbond_it2.571.51062
X-RAY DIFFRACTIONr_mcangle_it2.96321668
X-RAY DIFFRACTIONr_scbond_it4.3333618
X-RAY DIFFRACTIONr_scangle_it6.3834.5500
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 784 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.420.5
medium thermal2.412
LS refinement shellResolution: 2.376→2.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 30 -
Rwork0.222 519 -
obs--77.87 %

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