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- PDB-1i5g: TRYPAREDOXIN II COMPLEXED WITH GLUTATHIONYLSPERMIDINE -

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Basic information

Entry
Database: PDB / ID: 1i5g
TitleTRYPAREDOXIN II COMPLEXED WITH GLUTATHIONYLSPERMIDINE
ComponentsTRYPAREDOXIN II
KeywordsELECTRON TRANSPORT / tryparedoxin
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) activity / negative regulation of Wnt signaling pathway / negative regulation of protein ubiquitination / nucleus
Similarity search - Function
TryX and NRX, thioredoxin domain / Thioredoxin-like / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONYLSPERMIDINE / Tryparedoxin II
Similarity search - Component
Biological speciesCrithidia fasciculata (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHofmann, B. / Budde, H. / Bruns, K. / Guerrero, S.A. / Kalisz, H.M. / Menge, U. / Montemartini, M. / Nogoceke, E. / Steinert, P. / Wissing, J.B. ...Hofmann, B. / Budde, H. / Bruns, K. / Guerrero, S.A. / Kalisz, H.M. / Menge, U. / Montemartini, M. / Nogoceke, E. / Steinert, P. / Wissing, J.B. / Flohe, L. / Hecht, H.-J.
CitationJournal: Biol.Chem. / Year: 2001
Title: Structures of tryparedoxins revealing interaction with trypanothione.
Authors: Hofmann, B. / Budde, H. / Bruns, K. / Guerrero, S.A. / Kalisz, H.M. / Menge, U. / Montemartini, M. / Nogoceke, E. / Steinert, P. / Wissing, J.B. / Flohe, L. / Hecht, H.J.
History
DepositionFeb 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRYPAREDOXIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7803
Polymers16,2241
Non-polymers5572
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.211, 50.510, 67.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRYPAREDOXIN II


Mass: 16223.512 Da / Num. of mol.: 1 / Mutation: C44S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crithidia fasciculata (eukaryote) / Strain: HS6 / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: O77093
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-TS5 / GLUTATHIONYLSPERMIDINE


Mass: 434.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H34N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: PEG 8000, Mes Tris glutathionylspermidine, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
129 %PEG80001reservoirpH6.9
20.1MES/Tris1reservoir
30.1 Mammonium sulfate1drop
42.5 mMN1-glutathionylspermidine1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.95 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 25, 2000 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.4→28.87 Å / Num. all: 24911 / Num. obs: 24911 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.065 / Net I/σ(I): 4.6
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 8.8 / Num. unique all: 3735 / Rsym value: 0.077 / % possible all: 92.1
Reflection
*PLUS
Num. obs: 24680 / % possible obs: 89 % / Rmerge(I) obs: 0.065

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FG4

1fg4


Resolution: 1.4→40.49 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1229 4.9 %RANDOM
Rwork0.168 ---
all0.17 24911 --
obs0.1703 23682 87.87 %-
Displacement parametersBiso mean: 7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3----0 Å2
Refine analyzeLuzzati coordinate error free: 0.075 Å
Refinement stepCycle: LAST / Resolution: 1.4→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1147 0 37 279 1463
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_d0.0131.098
X-RAY DIFFRACTIONp_mcangle_d2.3981.789
X-RAY DIFFRACTIONp_scbond_d1.481
X-RAY DIFFRACTIONp_scangle_d2.292
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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