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- PDB-4b1b: Crystal structure of Plasmodium falciparum oxidised Thioredoxin R... -

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Basic information

Entry
Database: PDB / ID: 4b1b
TitleCrystal structure of Plasmodium falciparum oxidised Thioredoxin Reductase at 2.9 angstrom
ComponentsTHIOREDOXIN REDUCTASE
KeywordsOXIDOREDUCTASE / FAD / NADPH / THIOL-MEDIATED REDOX METABOLISM / CLASS-I PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE / MALARIA
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / : / Pyridine nucleotide-disulphide oxidoreductase, class I / 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 ...Thioredoxin/glutathione reductase selenoprotein / : / Pyridine nucleotide-disulphide oxidoreductase, class I / 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 / 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 speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBoumis, G. / Giardina, G. / Dimastrogiovanni, D. / Angelucci, F. / Saccoccia, F. / Brunori, M. / Bellelli, A. / Miele, A.E.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Crystal Structure of Plasmodium Falciparum Thioredoxin Reductase, a Validated Drug Target.
Authors: Boumis, G. / Giardina, G. / Angelucci, F. / Bellelli, A. / Brunori, M. / Dimastrogiovanni, D. / Saccoccia, F. / Miele, A.E.
History
DepositionJul 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET SHEET RECORDS MODIFIED TO REPRESENT AUTHORS' DETAILED ANALYSIS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN REDUCTASE
B: THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,1334
Polymers119,5622
Non-polymers1,5712
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-49 kcal/mol
Surface area37470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.187, 109.242, 182.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein THIOREDOXIN REDUCTASE / TRXR


Mass: 59781.160 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: ISOLATE FCH-5 / Plasmid: PGEX-4T-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q25861, thioredoxin-disulfide reductase (NADPH)
#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.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsADDITIONAL GLY -1 AND SER 0 ARE DERIVED FROM FUSION TAG CLEAVAGE. MET 1 IS MISSING DUE TO INSERTION ...ADDITIONAL GLY -1 AND SER 0 ARE DERIVED FROM FUSION TAG CLEAVAGE. MET 1 IS MISSING DUE TO INSERTION INTO THE EXPRESSION VECTOR PGEX-4T-1. CYS 2 IS THE FIRST RESIDUE OF THE WT PROTEIN.

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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: 2.58 Å3/Da / Density % sol: 52.34 % / Description: NONE
Crystal growpH: 8.5
Details: 16% (W/V) PEG 4000, 0.1 M TRIS/HCL, PH 8.5, 0.2 M SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.9→15.67 Å / Num. obs: 27908 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 9.23
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.02 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZKQ

1zkq


Resolution: 2.9→46.91 Å / Cor.coef. Fo:Fc: 0.856 / Cor.coef. Fo:Fc free: 0.83 / SU B: 19.092 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES -1 TO 37, 175-17, 428-456, 506-541 HAVE NOT BEEN MODELLED BECAUSE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.28805 1394 5 %RANDOM
Rwork0.26528 ---
obs0.26642 26474 96.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.254 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--1.98 Å20 Å2
3----2.34 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6772 0 106 3 6881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.026984
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.3921.9929443
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4395865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.04924.783276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.241151246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5661522
X-RAY DIFFRACTIONr_chiral_restr0.0280.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0215092
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.899→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 89 -
Rwork0.351 1655 -
obs--88.39 %

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