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- PDB-7dio: Structure of PfGrx1 with iron -

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Basic information

Entry
Database: PDB / ID: 7dio
TitleStructure of PfGrx1 with iron
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / REDOX ENZYME / TRX FOLD / GLUTATHIONE / MR-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. / 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 / MIRAS / Resolution: 1.899 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 1.1Oct 23, 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)12,8765
Polymers12,4361
Non-polymers4394
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area5950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.142, 48.142, 82.832
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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
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: 293 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 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.899→50 Å / Num. obs: 9229 / % possible obs: 99.9 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.089 / Χ2: 1.469 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.9-1.9311.40.5764421.0791100
1.93-1.9711.40.4924341.1251100
1.97-2.0111.40.3994681.2691100
2.01-2.0511.50.3774421.2811100
2.05-2.0911.40.3294721.3041100
2.09-2.1411.40.2654411.411100
2.14-2.1911.40.2324551.3321100
2.19-2.2511.60.2144401.4491100
2.25-2.3211.30.194661.4431100
2.32-2.3911.70.1584581.4991100
2.39-2.4811.50.1474451.4421100
2.48-2.5811.60.1284551.3541100
2.58-2.711.60.1184611.4971100
2.7-2.8411.60.0924651.4231100
2.84-3.0211.60.0784701.4671100
3.02-3.2511.70.0644561.5421100
3.25-3.5811.50.0554731.5951100
3.58-4.0911.50.0494721.8231100
4.09-5.1611.20.054852.0791100
5.16-5010.30.0675291.881198.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
Auto-Rickshawphasing
PHASERphasing
SHELXEmodel building
RESOLVEmodel building
RefinementMethod to determine structure: MIRAS / Resolution: 1.899→24.071 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2045 437 4.75 %
Rwork0.1452 8765 -
obs0.1478 9202 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.78 Å2 / Biso mean: 24.668 Å2 / Biso min: 12.52 Å2
Refinement stepCycle: final / Resolution: 1.899→24.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms824 0 23 124 971
Biso mean--34.28 36.72 -
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
1.8992-2.17380.2161620.14722824
2.1738-2.73820.20381270.16182910
2.7382-24.0710.20081480.13743031
Refinement TLS params.Method: refined / Origin x: -23.1769 Å / Origin y: 10.0354 Å / Origin z: -5.2084 Å
111213212223313233
T0.1307 Å2-0.0093 Å20.0072 Å2-0.1372 Å2-0.0008 Å2--0.1026 Å2
L2.1353 °2-0.7755 °20.541 °2-2.324 °2-0.0599 °2--1.2222 °2
S-0.0503 Å °-0.043 Å °0.0315 Å °0.0347 Å °0.0197 Å °-0.0207 Å °-0.0373 Å °0.0382 Å °0.0322 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 202
2X-RAY DIFFRACTION1allA301 - 302
3X-RAY DIFFRACTION1allS1 - 122

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