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- PDB-1bzl: CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI TRYPANOTHIONE REDUCTASE IN... -

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Basic information

Entry
Database: PDB / ID: 1bzl
TitleCRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI TRYPANOTHIONE REDUCTASE IN COMPLEX WITH TRYPANOTHIONE, AND THE STRUCTURE-BASED DISCOVERY OF NEW NATURAL PRODUCT INHIBITORS
ComponentsTRYPANOTHIONE REDUCTASE (OXIDIZED FORM)
KeywordsOXIDOREDUCTASE / TRYPANOTHIONE REDUCTASE / FAD DEPENDENT DISULPHIDE OXIDOREDUCTASE
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 / BIS(GAMMA-GLUTAMYL-CYSTEINYL-GLYCINYL)SPERMIDINE / Trypanothione reductase / Trypanothione reductase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsBond, C.S. / Zhang, Y. / Berriman, M. / Cunningham, M. / Fairlamb, A.H. / Hunter, W.N.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of Trypanosoma cruzi trypanothione reductase in complex with trypanothione, and the structure-based discovery of new natural product inhibitors.
Authors: Bond, C.S. / Zhang, Y. / Berriman, M. / Cunningham, M.L. / Fairlamb, A.H. / Hunter, W.N.
History
DepositionNov 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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
Revision 1.4Oct 16, 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: TRYPANOTHIONE REDUCTASE (OXIDIZED FORM)
B: TRYPANOTHIONE REDUCTASE (OXIDIZED FORM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6336
Polymers106,6142
Non-polymers3,0194
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12110 Å2
ΔGint-95 kcal/mol
Surface area36270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.330, 93.330, 157.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Cell settingtetragonal
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.979957, 0.199187, -0.002999), (0.198788, 0.978751, 0.050298), (0.012955, 0.048694, -0.99873)
Vector: 84.468, -8.439, -0.127)

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Components

#1: Protein TRYPANOTHIONE REDUCTASE (OXIDIZED FORM) / EC 1.6.4.8 / TR


Mass: 53306.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: BRAZILIAN SILVIO STRAIN CLONE X10-1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q26970, UniProt: P28593*PLUS, 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: Chemical ChemComp-GCG / BIS(GAMMA-GLUTAMYL-CYSTEINYL-GLYCINYL)SPERMIDINE / TRYPANOTHIONE


Mass: 723.862 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H49N9O10S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 3.17 Å3/Da / Density % sol: 61 %
Crystal growpH: 6 / Details: pH 6.0
Components of the solutions
IDNameCrystal-IDSol-ID
1MALEIC BUFFER11
2PEG 400011
3PEG 400012
Crystal grow
*PLUS
Method: other / Details: Zhang, Y., (1993) J. Mol. Biol., 233, 1217.
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1991
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 45818 / % possible obs: 87.4 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.75 / Rsym value: 0.75 / Net I/σ(I): 6
Reflection shellResolution: 2.4→2.53 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.275 / % possible all: 86
Reflection
*PLUS
Num. measured all: 142903

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
X-PLORmodel building
X-PLOR3.1refinement
CCP4data scaling
X-PLORphasing
RefinementStarting model: PDB ENTRY 1TYT

1tyt


Resolution: 2.4→8 Å / Isotropic thermal model: RESTRAINED / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.209 --
obs-45818 87.4 %
Displacement parametersBiso mean: 32.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7459 0 202 409 8070
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg2.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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