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- PDB-1nda: THE STRUCTURE OF TRYPANOSOMA CRUZI TRYPANOTHIONE REDUCTASE IN THE... -

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Basic information

Entry
Database: PDB / ID: 1nda
TitleTHE STRUCTURE OF TRYPANOSOMA CRUZI TRYPANOTHIONE REDUCTASE IN THE OXIDIZED AND NADPH REDUCED STATE
ComponentsTRYPANOTHIONE OXIDOREDUCTASE
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 speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 3.3 Å
AuthorsLantwin, C.B. / Kabsch, W. / Pai, E.F. / Schlichting, I. / Krauth-Siegel, R.L.
Citation
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.
#1: Journal: FEBS Lett. / Year: 1993
Title: Crystallization and Preliminary Crystallographic Analysis of Trypanothione Reductase from Trypanosoma Cruzi, the Causative Agent of Chagas' Disease
Authors: Krauth-Siegel, R.L. / Sticherling, C. / Jost, I. / Walsh, C.T. / Pai, E.F. / Kabsch, W. / Lantwin, C.B.
History
DepositionJul 2, 1993Processing site: BNL
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPANOTHIONE OXIDOREDUCTASE
B: TRYPANOTHIONE OXIDOREDUCTASE
C: TRYPANOTHIONE OXIDOREDUCTASE
D: TRYPANOTHIONE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,3328
Polymers215,1904
Non-polymers3,1424
Water00
1
A: TRYPANOTHIONE OXIDOREDUCTASE
B: TRYPANOTHIONE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1664
Polymers107,5952
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-79 kcal/mol
Surface area33780 Å2
MethodPISA
2
C: TRYPANOTHIONE OXIDOREDUCTASE
D: TRYPANOTHIONE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1664
Polymers107,5952
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9400 Å2
ΔGint-78 kcal/mol
Surface area33800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.300, 91.100, 126.000
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: PRO A 42 - PRO A 43 OMEGA = 35.35 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ASN A 352 - PRO A 353 OMEGA = 144.94 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO A 369 / 4: CIS PROLINE - PRO A 461
5: PRO B 42 - PRO B 43 OMEGA = 35.38 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: ASN B 352 - PRO B 353 OMEGA = 144.93 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: CIS PROLINE - PRO B 369 / 8: CIS PROLINE - PRO B 461
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.11639, -0.0086, -0.9932), (-0.01475, 0.99983, -0.0104), (0.99309, 0.0158, 0.1163)
Vector: 124.49, -24.23, -5.88)
DetailsTHE ASYMMETRIC UNIT CONTAINS FOUR MONOMERS. TWO MONOMERS ARE PRESENTED IN THIS ENTRY WITH CHAIN IDENTIFIERS *A* AND *B*. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE OTHER TWO MONOMERS IN THE ASYMMETRIC UNIT.

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Components

#1: Protein
TRYPANOTHIONE OXIDOREDUCTASE


Mass: 53797.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / References: UniProt: P28593
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
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: 3.62 Å3/Da / Density % sol: 66.07 %
Crystal grow
*PLUS
pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.2 Msodium citrate11
220 mMTris-HCl11
31 mMEDTA11
42 %octanoyl-N-methylglucamide11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.3 Å / Num. all: 46716 / Num. obs: 41811 / % possible obs: 89.5 % / Num. measured all: 88764 / Rmerge(I) obs: 0.127

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.206 / Rfactor obs: 0.206 / Highest resolution: 3.3 Å / σ(F): 1
Refinement stepCycle: LAST / Highest resolution: 3.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14804 0 212 0 15016
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_deg1.3
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.3

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