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- PDB-1vdc: STRUCTURE OF NADPH DEPENDENT THIOREDOXIN REDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1vdc
TitleSTRUCTURE OF NADPH DEPENDENT THIOREDOXIN REDUCTASE
ComponentsNADPH DEPENDENT THIOREDOXIN REDUCTASE
KeywordsOXIDOREDUCTASE / HYPOTHETICAL PROTEIN / REDOX-ACTIVE CENTER / DISULFIDE OXIDOREDUCTASE / THIOREDOXIN REDUCTASE / FLAVIN ADENINE DINULEOTIDE
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / chloroplast envelope / thioredoxin-disulfide reductase (NADPH) activity / positive regulation of cell division / removal of superoxide radicals / mitochondrion / plasma membrane / cytosol
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / : / 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 1, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDai, S. / Eklund, H.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of Arabidopsis thaliana NADPH dependent thioredoxin reductase at 2.5 A resolution.
Authors: Dai, S. / Saarinen, M. / Ramaswamy, S. / Meyer, Y. / Jacquot, J.P. / Eklund, H.
#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 Junior, C.H. / Kuriyan, J.
History
DepositionSep 22, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_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 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH DEPENDENT THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3023
Polymers35,4201
Non-polymers8822
Water5,873326
1
A: NADPH DEPENDENT THIOREDOXIN REDUCTASE
hetero molecules

A: NADPH DEPENDENT THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6036
Polymers70,8402
Non-polymers1,7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area7950 Å2
ΔGint-60 kcal/mol
Surface area25540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.974, 89.974, 175.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NADPH DEPENDENT THIOREDOXIN REDUCTASE / NTR


Mass: 35420.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: PET / Gene: ATTHIREDB / Plasmid: PET-3D / Gene (production host): ATTHIREDB / Production host: Escherichia coli (E. coli) / References: UniProt: Q39243, EC: 1.6.4.5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsNADPH CAN ALSO BE SEEN WITH LOW OCCUPANCY BUT NO COORDINATES ARE GIVEN FOR IT IN THIS ENTRY.
Sequence detailsPROTEIN SEQUENCE NUMBERING IS BASED ON E. COLI NTR SEQUENCE AND IS NOT THE SAME AS THE SEQUENCE ...PROTEIN SEQUENCE NUMBERING IS BASED ON E. COLI NTR SEQUENCE AND IS NOT THE SAME AS THE SEQUENCE NUMBERING IN GENBANK.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 5.05 Å3/Da / Density % sol: 70.6 %
Crystal growDetails: 7% ISOPROPANOL (OR 4% MPD) AND 1.8 M AMMONIUM SULFATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 %(v/v)isopropanol1reservoiror 4 % MPD
21.8 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 175 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Type: EMBL/DESY, HAMBURG / Wavelength: 0.857
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.857 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 25745 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.81 % / Biso Wilson estimate: 30.92 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.7
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.487 / % possible all: 100
Reflection
*PLUS
Num. obs: 20556 / Num. measured all: 139995
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TRB

1trb


Resolution: 2.5→20 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.243 2455 10 %
Rwork0.188 --
obs0.188 24816 100 %
Displacement parametersBiso mean: 31.6 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 58 326 2800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg
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
LS refinement shellResolution: 2.5→2.61 Å
RfactorNum. reflection% reflection
Rfree0.3279 303 9.649 %
Rwork0.3054 2818 -
obs--100 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_deg26.8

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