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- PDB-1fec: UNLIGANDED CRITHIDIA FASCICULATA TRYPANOTHIONE REDUCTASE AT 1.7 A... -

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Basic information

Entry
Database: PDB / ID: 1fec
TitleUNLIGANDED CRITHIDIA FASCICULATA TRYPANOTHIONE REDUCTASE AT 1.7 ANGSTROM RESOLUTION
ComponentsTRYPANOTHIONE REDUCTASE
KeywordsOXIDOREDUCTASE / REDOX-ACTIVE CENTER / FLAVOPROTEIN / FAD / NADP
Function / homology
Function and homology information


trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Trypanothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain ...Trypanothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Trypanothione reductase
Similarity search - Component
Biological speciesCrithidia fasciculata (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsStrickland, C. / Karplus, P.
Citation
Journal: To be Published
Title: Crithidia Fasciculata Trypanothione Reductase at 1.70 A Resolution
Authors: Strickland, C.L. / Karplus, P.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Overexpression of Crithidia Fasciculata Trypanothione Reductase and Crystallization Using a Novel Geometry
Authors: Strickland, C. / Puchalski, R. / Savvides, S. / Karplus, P.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1994
Title: Structure of Trypanothione Reductase from Crithidia Fasciculata at 2.6 A Resolution: Enzyme-Nadp Interactions of 2.8 A Resolution
Authors: Bailey, S. / Fairlamb, A. / Hunter, W.
#3: Journal: Proteins / Year: 1994
Title: The Structure of Trypanosoma Cruzi Trypanothione Reductase in the Oxidized and Nadph Reduced State
Authors: Lantwin, C.B. / Schlichting, I. / Kabsch, W. / Pai, E.F. / Krauth-Siegel, R.L.
#4: Journal: Eur.J.Biochem. / Year: 1993
Title: Substrate Interactions between Trypanothione Reductase and N1-Glutathionylspermidine Disulphide at 0.28-Nm Resolution
Authors: Bailey, S. / Smith, K. / Fairlamb, A.H. / Hunter, W.N.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: X-Ray Structure of Trypanothione Reductase from Crithidia Fasciculata at 2.4-A Resolution
Authors: Kuriyan, J. / Kong, X.P. / Krishna, T.S. / Sweet, R.M. / Murgolo, N.J. / Field, H. / Cerami, A. / Henderson, G.B.
History
DepositionJul 12, 1995Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_ref_seq_dif.details / _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: TRYPANOTHIONE REDUCTASE
B: TRYPANOTHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9234
Polymers106,3522
Non-polymers1,5712
Water17,799988
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-81 kcal/mol
Surface area35300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.800, 160.700, 60.000
Angle α, β, γ (deg.)90.00, 99.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRYPANOTHIONE REDUCTASE


Mass: 53176.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MONOCLINIC CRYSTAL FORM, DIMER IN THE ASYMMETRIC UNIT
Source: (gene. exp.) Crithidia fasciculata (eukaryote)
Description: SEE STRICKLAND, ET. AL. (1995) ACTA CRYST. D51, 337-341
Gene: TR1 / Plasmid: PET-TR1 / Gene (production host): TR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P39040, EC: 1.6.4.8
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 988 / 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

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 53 %

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 3, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionNum. obs: 103936 / % possible obs: 90 % / Observed criterion σ(I): 0.5 / Redundancy: 2.9 % / Rmerge(I) obs: 0.065

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.7→8 Å / σ(F): 1
RfactorNum. reflection
Rfree0.256 -
Rwork0.204 -
obs0.204 103936
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7452 0 106 987 8545
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.76
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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