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- PDB-7dir: Structure of PfGrx1 with mercury -

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Basic information

Entry
Database: PDB / ID: 7dir
TitleStructure of PfGrx1 with mercury
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / REDOX ENZYME / TRX FOLD / GLUTATHIONE / Hg-SAD
Function / homology
Function and homology information


protein-disulfide reductase (glutathione) activity / Interconversion of nucleotide di- and triphosphates / glutathione disulfide oxidoreductase activity / antioxidant activity / metal ion binding
Similarity search - Function
: / Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Thioredoxin-like superfamily
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.65 Å
AuthorsManickam, Y. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: To Be Published
Title: Interaction of metals with PfGrx1
Authors: Manickam, Y. / Sharma, A.
History
DepositionNov 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3666
Polymers12,4361
Non-polymers9295
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-19 kcal/mol
Surface area6070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.160, 48.160, 82.463
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0306300 / Plasmid: PQE30 / Production host: Escherichia coli M15 (bacteria)
References: UniProt: Q9NLB2, protein-disulfide reductase (glutathione)
#2: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


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


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.22 Å3/Da / Density % sol: 44.59 %
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, 0.02 M amino acids, 0.1 M MOPS/HEPES sodium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 13850 / % possible obs: 99.9 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.059 / Χ2: 1.59 / Net I/σ(I): 12.6 / Num. measured all: 107891
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.65-1.687.50.6826611.0711100
1.68-1.717.70.5956831.1791100
1.71-1.747.50.5226771.1781100
1.74-1.787.70.4146801.21100
1.78-1.827.60.366641.2161100
1.82-1.867.70.2996901.3231100
1.86-1.97.70.2446801.3711100
1.9-1.967.70.2136811.4261100
1.96-2.017.80.1616961.5191100
2.01-2.087.90.146871.6111100
2.08-2.157.80.1146711.6691100
2.15-2.247.90.16951.7141100
2.24-2.347.90.0856871.7441100
2.34-2.4680.0766921.831100
2.46-2.628.10.0686971.7921100
2.62-2.828.10.0587081.7381100
2.82-3.1180.0496981.8271100
3.11-3.5580.0437101.9261100
3.55-4.4880.0387212.0991100
4.48-507.30.0457722.119197.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SHELXDEphasing
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→24.08 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1846 691 5 %
Rwork0.1533 13133 -
obs0.1549 13824 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.8 Å2 / Biso mean: 27.4174 Å2 / Biso min: 16.12 Å2
Refinement stepCycle: final / Resolution: 1.65→24.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms835 0 24 123 982
Biso mean--36.61 40.35 -
Num. residues----107
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.6503-1.77770.25861490.22272554
1.7777-1.95650.25761230.1762585
1.9565-2.23940.18031370.15582606
2.2394-2.82080.17521390.15672641
2.8208-24.080.17051430.14062747
Refinement TLS params.Method: refined / Origin x: 23.0883 Å / Origin y: -9.877 Å / Origin z: -5.108 Å
111213212223313233
T0.208 Å2-0.0068 Å20.0067 Å2-0.2109 Å2-0.0031 Å2--0.1929 Å2
L1.4733 °2-0.6558 °2-0.1983 °2-1.9288 °20.0796 °2--1.5002 °2
S-0.0638 Å °-0.0543 Å °-0.0367 Å °0.0829 Å °0.0414 Å °0.0415 Å °0.0211 Å °-0.0435 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 202
2X-RAY DIFFRACTION1allA301 - 303
3X-RAY DIFFRACTION1allS1 - 123

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