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- PDB-1xwa: Drospohila thioredoxin, oxidized, P41212 -

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Basic information

Entry
Database: PDB / ID: 1xwa
TitleDrospohila thioredoxin, oxidized, P41212
Componentsthioredoxin
KeywordsELECTRON TRANSPORT / Dimerization / Drosophila melanogaster / redox regulation / thioredoxin / x-ray crystal structure
Function / homology
Function and homology information


The NLRP3 inflammasome / TP53 Regulates Metabolic Genes / Protein repair / Detoxification of Reactive Oxygen Species / Interconversion of nucleotide di- and triphosphates / Oxidative Stress Induced Senescence / glutathione disulfide oxidoreductase activity / disulfide oxidoreductase activity / protein-disulfide reductase activity / cell redox homeostasis ...The NLRP3 inflammasome / TP53 Regulates Metabolic Genes / Protein repair / Detoxification of Reactive Oxygen Species / Interconversion of nucleotide di- and triphosphates / Oxidative Stress Induced Senescence / glutathione disulfide oxidoreductase activity / disulfide oxidoreductase activity / protein-disulfide reductase activity / cell redox homeostasis / determination of adult lifespan / response to oxidative stress / nucleus / 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 speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWahl, M.C. / Irmler, A. / Hecker, B. / Schirmer, R.H. / Becker, K.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Comparative structural analysis of oxidized and reduced thioredoxin from Drosophila melanogaster
Authors: Wahl, M.C. / Irmler, A. / Hecker, B. / Schirmer, R.H. / Becker, K.
History
DepositionOct 29, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: thioredoxin
B: thioredoxin
C: thioredoxin
D: thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7898
Polymers48,4164
Non-polymers3734
Water7,530418
1
A: thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4775
Polymers12,1041
Non-polymers3734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,1041
Polymers12,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,1041
Polymers12,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,1041
Polymers12,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: thioredoxin
hetero molecules

D: thioredoxin

B: thioredoxin

C: thioredoxin


Theoretical massNumber of molelcules
Total (without water)48,7898
Polymers48,4164
Non-polymers3734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454y-1/2,-x+1/2,z-1/41
crystal symmetry operation6_555x+1/2,-y+1/2,-z+3/41
crystal symmetry operation7_556y,x,-z+11
Buried area3530 Å2
ΔGint-49 kcal/mol
Surface area19520 Å2
MethodPISA
6
A: thioredoxin
hetero molecules

B: thioredoxin


Theoretical massNumber of molelcules
Total (without water)24,5816
Polymers24,2082
Non-polymers3734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x+1/2,-y+1/2,-z+3/41
Buried area1010 Å2
ΔGint-33 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.544, 92.544, 97.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
thioredoxin


Mass: 12104.024 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: TRX-2 / Plasmid: pQE-30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9V429
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: CdCl2, PEG400, pH 4.6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 37273 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 35 Å2 / Rsym value: 0.038 / Net I/σ(I): 21.1
Reflection shellResolution: 2.1→2.2 Å / % possible all: 88.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1AUC

1auc


Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1604 -Random
Rwork0.226 ---
obs-32287 95 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 4 418 3731

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