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- PDB-1trb: CONVERGENT EVOLUTION OF SIMILAR FUNCTION IN TWO STRUCTURALLY DIVE... -

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Basic information

Entry
Database: PDB / ID: 1trb
TitleCONVERGENT EVOLUTION OF SIMILAR FUNCTION IN TWO STRUCTURALLY DIVERGENT ENZYMES
ComponentsTHIOREDOXIN REDUCTASE
KeywordsOXIDOREDUCTASE(FLAVOENZYME)
Function / homology
Function and homology information


thioredoxin-disulfide reductase complex / thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / flavin adenine dinucleotide binding / cytosol
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / Pyridine nucleotide-disulphide oxidoreductase / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / Pyridine nucleotide-disulphide oxidoreductase / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsKuriyan, J. / Krishna, T.S.R.
Citation
Journal: Nature / Year: 1991
Title: Convergent evolution of similar function in two structurally divergent enzymes.
Authors: Kuriyan, J. / Krishna, T.S. / Wong, L. / Guenther, B. / Pahler, A. / Williams Jr., C.H. / Model, P.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Crystallization and Preliminary X-Ray Characterization of Thioredoxin Reductase from Escherichia Coli
Authors: Kuriyan, J. / Wong, L. / Russel, M. / Model, P.
History
DepositionSep 7, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2992
Polymers34,5141
Non-polymers7861
Water2,954164
1
A: THIOREDOXIN REDUCTASE
hetero molecules

A: THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5994
Polymers69,0272
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8580 Å2
ΔGint-39 kcal/mol
Surface area24210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.100, 123.100, 81.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Atom site foot note1: RESIDUE PRO 93 IS A CIS PROLINE.
DetailsTHE FOLLOWING CRYSTALLOGRAPHIC SYMMETRY OPERATION WILL WILL YIELD COORDINATES FOR THE SECOND CHAIN IN THE DIMER: -0.500000 0.866000 0.000000 0.000000 0.866000 0.500000 0.000000 0.000000 0.000000 0.000000 -1.000000 0.000000

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Components

#1: Protein THIOREDOXIN REDUCTASE


Mass: 34513.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A9P4, EC: 1.6.4.5
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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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: 52.3 %
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 7 / PH range high: 6.5 / Details: 'Kuriyan, J.', (1989) J. Biol. Chem., 264, 12752.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
135 %PEG33001reservoir
2200 mMammonium sulfate1reservoiror 200 mM lithium sulfate
350 mMMES1reservoiror HEPES
420 mg/mlprotein1drop
560 mMdithiothreitol1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 95 % / Rmerge(I) obs: 0.005

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.177 / Rfactor obs: 0.177 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 53 164 2611
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection obs: 21106 / σ(I): 2 / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0019
X-RAY DIFFRACTIONx_angle_deg3.2

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