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- PDB-2tpr: X-RAY STRUCTURE OF TRYPANOTHIONE REDUCTASE FROM CRITHIDIA FASCICU... -

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Basic information

Entry
Database: PDB / ID: 2tpr
TitleX-RAY STRUCTURE OF TRYPANOTHIONE REDUCTASE FROM CRITHIDIA FASCICULATA AT 2.4 ANGSTROMS RESOLUTION
ComponentsTRYPANOTHIONE REDUCTASE
KeywordsOXIDOREDUCTASE
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 / Resolution: 2.4 Å
AuthorsKuriyan, J. / Kong, X.-P. / Krishna, T.S.R.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Preliminary Crystallographic Analysis of Trypanothione Reductase from Crithidia Fasciculata
Authors: Kuriyan, J. / Wong, L. / Guenther, B.D. / Murgolo, N.J. / Cerami, A. / Henderson, G.B.
#2: Journal: Biochemistry / Year: 1986
Title: Purification and Characterization of Trypanothione Reductase from Crithidia Fasciculata, a Newly Discovered Member of the Family of Disulfide-Containing Flavoprotein Reductases
Authors: Shames, S.L. / Fairlamb, A.H. / Cerami, A. / Walsh, C.T.
History
DepositionAug 22, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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 20, 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: TRYPANOTHIONE REDUCTASE
B: TRYPANOTHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8274
Polymers106,2562
Non-polymers1,5712
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-82 kcal/mol
Surface area34880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.000, 161.800, 61.500
Angle α, β, γ (deg.)90.00, 104.10, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 42 / 2: CIS PROLINE - PRO A 369 / 3: CIS PROLINE - PRO A 461 / 4: CIS PROLINE - PRO B 42 / 5: CIS PROLINE - PRO B 369 / 6: CIS PROLINE - PRO B 461

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Components

#1: Protein TRYPANOTHIONE REDUCTASE


Mass: 53127.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crithidia fasciculata (eukaryote) / 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.: 350 / 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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 %(w/v)PEG80001reservoir
20.1 Mammonium sulfate1reservoir
360-100 mMdithiothreitol1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 42201 / % possible obs: 88 % / Num. measured all: 131449 / Rmerge(I) obs: 0.079

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.18 / Rfactor obs: 0.18 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7316 0 106 350 7772
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg2.7
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
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 6 Å / Num. reflection obs: 33134 / σ(F): 2 / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.7

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