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- PDB-1onf: Crystal structure of Plasmodium falciparum Glutathione reductase -

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Basic information

Entry
Database: PDB / ID: 1onf
TitleCrystal structure of Plasmodium falciparum Glutathione reductase
ComponentsGlutathione reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


glutathione-disulfide reductase / 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
: / 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 ...: / 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 / Glutathione reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSarma, G.N. / Savvides, S.N. / Becker, K. / Schirmer, M. / Schirmer, R.H. / Karplus, P.A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Glutathione reductase of the malarial parasite Plasmodium falciparum: Crystal structure and inhibitor development
Authors: Sarma, G.N. / Savvides, S.N. / Becker, K. / Schirmer, M. / Schirmer, R.H. / Karplus, P.A.
History
DepositionFeb 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4252
Polymers56,6391
Non-polymers7861
Water77543
1
A: Glutathione reductase
hetero molecules

A: Glutathione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8494
Polymers113,2782
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566x,-y+1,-z+3/21
Buried area10080 Å2
ΔGint-67 kcal/mol
Surface area37080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.640, 90.640, 123.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Glutathione reductase / GR / GRase


Mass: 56638.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: GR2 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): SG5(DE3)
References: UniProt: Q94655, glutathione-disulfide reductase
#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.: 43 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.31 %
Crystal growpH: 9 / Details: pH 9.0
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 mMEDTA1droppH7.0
210 mg/mlprotein1drop
314 %(w/v)PEG550 MME1reservoir
470 mM1reservoirNaCl
570 mMBicine1reservoirpH8.7-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 16434 / % possible obs: 98.7 % / Redundancy: 7.5 % / Net I/σ(I): 13.5
Reflection shellResolution: 2.6→2.78 Å / Mean I/σ(I) obs: 4.1 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.388

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GRS

3grs


Resolution: 2.6→29.36 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.882 / SU B: 14.747 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: R and R-free values are different from the publication because the structure was refined further prior to pdb submission. Refinement was carried out by fixing the residue A GLU 31 to avoid ...Details: R and R-free values are different from the publication because the structure was refined further prior to pdb submission. Refinement was carried out by fixing the residue A GLU 31 to avoid it moving to create a close contact with the AO2* and AO3* atoms of the FAD
RfactorNum. reflection% reflectionSelection details
Rfree0.2969 1575 10.1 %RANDOM
Rwork0.25558 ---
obs0.25981 14029 95.78 %-
all-16434 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.087 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3457 0 52 43 3552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223570
X-RAY DIFFRACTIONr_angle_refined_deg2.0931.9814823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4763433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.78315673
X-RAY DIFFRACTIONr_chiral_restr0.1420.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022619
X-RAY DIFFRACTIONr_nbd_refined0.3180.31775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.5253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.372
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.55
X-RAY DIFFRACTIONr_mcbond_it0.6621.52171
X-RAY DIFFRACTIONr_mcangle_it1.18723513
X-RAY DIFFRACTIONr_scbond_it2.25931399
X-RAY DIFFRACTIONr_scangle_it3.4814.51310
LS refinement shellResolution: 2.604→2.671 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.342 97
Rwork0.259 943
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.17171.9338-0.64853.6247-1.00751.11620.00130.05830.78230.22140.06820.2482-0.52810.1381-0.06950.2578-0.0663-0.01190.176-0.030.333370.05467.0986.476
21.35160.16030.95583.6430.2384.239-0.40850.45940.2986-0.59370.32160.1361-0.59190.07090.08690.2662-0.20110.00580.3340.05330.137263.89452.54266.698
34.13351.8497-1.88426.81510.08261.0314-0.16260.57250.3871-0.64460.2407-0.6587-0.32921.0639-0.07810.3447-0.34150.07260.57750.04070.52289.16969.85576.227
43.2272-0.1213-0.80561.1188-1.07942.7099-0.08970.398-0.3743-0.18680.0468-0.36410.12110.6650.0430.03450.05120.05330.3603-0.11070.209581.17238.42584.039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1482 - 149
2X-RAY DIFFRACTION2AA149 - 275150 - 276
3X-RAY DIFFRACTION3AA276 - 378277 - 379
4X-RAY DIFFRACTION4AA379 - 495380 - 496
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.302 / Rfactor Rwork: 0.251
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.1
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.78 Å / Rfactor Rfree: 0.37 / Rfactor Rwork: 0.285

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