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- PDB-7diz: Structure of PfGrx1 in the reduced state using DTT -

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Basic information

Entry
Database: PDB / ID: 7diz
TitleStructure of PfGrx1 in the reduced state using DTT
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / REDOX ENZYME / TRX FOLD / GLUTATHIONE / Reduced state
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. / 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
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)12,7643
Polymers12,4361
Non-polymers3272
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-9 kcal/mol
Surface area5940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.357, 48.357, 82.383
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 292 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: 1.8→50 Å / Num. obs: 10836 / % possible obs: 99.9 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.041 / Χ2: 1.047 / Net I/σ(I): 16.5 / Num. measured all: 89835
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.837.50.2365370.9071100
1.83-1.868.30.2085280.941100
1.86-1.98.10.1825111.0091100
1.9-1.948.40.1515351.0031100
1.94-1.988.20.1315190.9891100
1.98-2.038.40.1145521.0521100
2.03-2.088.30.09651911100
2.08-2.138.40.0885261.1021100
2.13-2.28.50.0755511.1111100
2.2-2.278.30.0715371.0511100
2.27-2.358.40.065171.091100
2.35-2.448.50.0585461.0841100
2.44-2.558.50.0535401.0631100
2.55-2.698.50.0495401.0661100
2.69-2.868.40.0435421.0911100
2.86-3.088.40.0365471.0441100
3.08-3.398.50.0325461.031100
3.39-3.888.40.0285601.0221100
3.88-4.888.30.0265741.0631100
4.88-507.70.0296091.193198.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HJM

4hjm


Resolution: 1.8→24.178 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1767 522 4.83 %
Rwork0.1561 10286 -
obs0.1571 10808 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.9 Å2 / Biso mean: 22.8965 Å2 / Biso min: 11.21 Å2
Refinement stepCycle: final / Resolution: 1.8→24.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 21 99 946
Biso mean--31.66 35.35 -
Num. residues----106
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8-1.9810.21211200.17342512
1.981-2.26750.1731310.15082546
2.2675-2.85610.19621450.15842535
2.8561-24.1780.15921260.15332693
Refinement TLS params.Method: refined / Origin x: -22.96 Å / Origin y: 10.0186 Å / Origin z: -5.0823 Å
111213212223313233
T0.1502 Å2-0.0119 Å2-0.0063 Å2-0.1406 Å20.003 Å2--0.1246 Å2
L1.6928 °2-0.7452 °20.3061 °2-2.0218 °2-0.1102 °2--1.1725 °2
S-0.055 Å °0.0068 Å °0.0664 Å °0.0944 Å °0.0146 Å °-0.084 Å °-0.0369 Å °0.043 Å °0.0513 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 111
2X-RAY DIFFRACTION1allA201 - 202
3X-RAY DIFFRACTION1allS1 - 92

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