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- PDB-4n11: Crystal structure of plasmodium falciparum reduced glutaredoxin 1... -

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Basic information

Entry
Database: PDB / ID: 4n11
TitleCrystal structure of plasmodium falciparum reduced glutaredoxin 1 (PfGrx1) complexed with cisplatin
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / Glutathione / Active site / TRX FOLD / Redox Enzyme / Pt-SAD / cisplatin
Function / homology
Function and homology information


protein-disulfide reductase (glutathione) activity / Interconversion of nucleotide di- and triphosphates / glutathione disulfide oxidoreductase activity / antioxidant activity
Similarity search - Function
: / Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin ...: / Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cisplatin / Glutaredoxin-1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.97 Å
AuthorsYogavel, M. / Sharma, A.
CitationJournal: To be Published
Title: Interaction of Cisplatin with plasmodium falciparum Glutaredoxin 1
Authors: Yogavel, M. / Tripathi, T. / Rahlfs, S. / Becker, K. / Sharma, A.
History
DepositionOct 3, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1825
Polymers12,4361
Non-polymers7464
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.478, 48.478, 82.391
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Glutaredoxin / / Glutaredoxin 1


Mass: 12436.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: GRX1 / Plasmid: pQE30 / Production host: Escherichia Coli (E. coli) / Strain (production host): M15
References: UniProt: Q9NLB2, arsenate reductase (glutathione/glutaredoxin)
#2: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID / MOPS


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum / Cisplatin


Mass: 300.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication, chemotherapy*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.25 Å3/Da / Density % sol: 45.27 % / Mosaicity: 1.599 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12.5%(W/V) PEG1000, 12.5%(W/V) PEG3350, 12.5%(V/V) MPD, 0.02M AMINO ACIDS, 0.1M MOPS/HEPES SODIUM,, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 17, 2013 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. all: 8380 / Num. obs: 8372 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10 % / Biso Wilson estimate: 27.99 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.247 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.97-28.50.5554161.027199.3
2-2.04100.563971.0971100
2.04-2.0810.10.4724101.11100
2.08-2.12100.4044131.1181100
2.12-2.17100.3264011.1321100
2.17-2.229.90.2954251.1761100
2.22-2.2710.10.2663941.1721100
2.27-2.34100.2094081.1421100
2.34-2.410.10.1924161.3351100
2.4-2.4810.10.1834051.1911100
2.48-2.5710.20.1544261.1911100
2.57-2.6710.10.1274161.1381100
2.67-2.810.20.1074081.1741100
2.8-2.9410.30.0864121.2241100
2.94-3.1310.30.074241.221100
3.13-3.3710.30.0594261.2251100
3.37-3.7110.40.0434291.2771100
3.71-4.2410.20.0364221.3471100
4.24-5.3510.10.0374521.6021100
5.35-509.20.054721.929198.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→27.464 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8812 / SU ML: 0.16 / σ(F): 1.36 / Phase error: 18.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 821 9.84 %RANDOM
Rwork0.1569 ---
all0.1616 8353 --
obs0.1616 8346 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.7 Å2 / Biso mean: 27.4628 Å2 / Biso min: 15.33 Å2
Refinement stepCycle: LAST / Resolution: 1.97→27.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 33 80 956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01945
X-RAY DIFFRACTIONf_angle_d1.3271276
X-RAY DIFFRACTIONf_chiral_restr0.082141
X-RAY DIFFRACTIONf_plane_restr0.004159
X-RAY DIFFRACTIONf_dihedral_angle_d16.479374
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9703-2.09370.21261490.161112131362
2.0937-2.25530.19941270.145612171344
2.2553-2.48210.18331310.142912421373
2.4821-2.84090.22191420.149712491391
2.8409-3.5780.19971390.157312541393
3.578-27.46630.21811330.164713501483

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