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- PDB-1cl0: CRYSTAL STRUCTURE OF REDUCED THIOREDOXIN REDUCTASE FROM ESCHERICH... -

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Basic information

Entry
Database: PDB / ID: 1cl0
TitleCRYSTAL STRUCTURE OF REDUCED THIOREDOXIN REDUCTASE FROM ESCHERICHIA COLI.
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLennon, B.W. / Williams Jr, C.H. / Ludwig, M.L.
Citation
Journal: Protein Sci. / Year: 1999
Title: Crystal structure of reduced thioredoxin reductase from Escherichia coli: structural flexibility in the isoalloxazine ring of the flavin adenine dinucleotide cofactor.
Authors: Lennon, B.W. / Williams Jr., C.H. / Ludwig, M.L.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystal structure of Escherichia coli thioredoxin reductase refined at 2 A resolution. Implications for a large conformational change during catalysis.
Authors: Waksman, G. / Krishna, T.S. / Williams Jr., C.H. / Kuriyan, J.
History
DepositionMay 4, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Aug 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3152
Polymers34,5301
Non-polymers7861
Water1,964109
1
A: THIOREDOXIN REDUCTASE
hetero molecules

A: THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6314
Polymers69,0602
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8720 Å2
ΔGint-41 kcal/mol
Surface area24110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)121.298, 121.298, 81.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein THIOREDOXIN REDUCTASE


Mass: 34529.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FAD AND ACTIVE SITE DISULFIDE (CYS 135 AND CYS 138) REDUCED BY SODIUM DITHIONITE AFTER CRYSTALLIZATION
Source: (gene. exp.) Escherichia coli (E. coli) / Description: TRXB-STRAIN / Gene: TRXB / Plasmid: PTRR301 / Cellular location (production host): CYTOPLASM / Gene (production host): TRXB / Production host: Escherichia coli (E. coli) / Strain (production host): A326 / 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.: 109 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 50.8 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
219 mM1,12-dodecanedioic acid1drop
350 mMHEPES1reservoir
4200 mMammonium sulfate1reservoir
532-40 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 12009 / % possible obs: 96.5 % / Redundancy: 7.8 % / Biso Wilson estimate: 21.1 Å2 / Rsym value: 0.119 / Net I/σ(I): 9.5
Reflection shellResolution: 2.5→2.65 Å / Mean I/σ(I) obs: 2.1 / % possible all: 82.4
Reflection
*PLUS
Rmerge(I) obs: 0.119
Reflection shell
*PLUS
% possible obs: 82.4 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TDE

1tde


Resolution: 2.5→10 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED DISORDERED REGION (RESIDUES 225-230) WAS MODELED STEREOCHEMICALLY. A HYDROGEN BOND PROBABLY EXISTS BETWEEN THE GAMMA SULFURS OF RESIDUES CYS 135 AND CYS 138.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 729 6.1 %RANDOM
Rwork0.2 ---
obs-12009 96.5 %-
Displacement parametersBiso mean: 24.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 53 109 2558
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
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
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 96 5.7 %
Rwork0.282 1575 -
obs--82.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM_RED1.FADTOPH_RED1.FAD
X-RAY DIFFRACTION3PARAM.WATTOPH.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.18

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