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- PDB-7diu: Structure of PfGrx1 in the intermediate state with platinum and cesium -

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Basic information

Entry
Database: PDB / ID: 7diu
TitleStructure of PfGrx1 in the intermediate state with platinum and cesium
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / REDOX ENZYME / TRX FOLD / GLUTATHIONE / Pt-SAD / Cs-SAD
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. / Thioredoxin-like superfamily
Similarity search - Domain/homology
: / : / Glutaredoxin-1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.879 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3587
Polymers12,4361
Non-polymers9216
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-55 kcal/mol
Surface area5890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.584, 48.584, 82.721
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#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)

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Non-polymers , 5 types, 78 molecules

#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.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.72 %
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: Jun 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.879→50 Å / Num. obs: 17785 / % possible obs: 99.9 % / Redundancy: 20.7 % / Rmerge(I) obs: 0.066 / Χ2: 1.643 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.88-1.9120.30.5524681.1281100
1.91-1.9520.80.494771.131100
1.95-1.9820.50.4074531.1831100
1.98-2.0320.80.3434891.271100
2.03-2.0720.60.3054651.2871100
2.07-2.1220.80.2494931.361100
2.12-2.1720.90.2024541.4481100
2.17-2.2320.70.1754951.5531100
2.23-2.2921.10.1594651.551100
2.29-2.3720.80.1334761.6481100
2.37-2.45210.1164791.6511100
2.45-2.5521.10.1044891.6681100
2.55-2.67210.094751.6841100
2.67-2.8120.90.0764831.7921100
2.81-2.9821.20.0634851.8561100
2.98-3.21210.0554911.9671100
3.21-3.54210.0484932.0091100
3.54-4.0520.80.0424922.1061100
4.05-5.120.30.0435102.1561100
5.1-5018.30.0515512.279198.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
Auto-Rickshawphasing
Cootmodel building
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.879→27.574 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 1801 10.13 %
Rwork0.1563 15984 -
obs0.1598 17785 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.13 Å2 / Biso mean: 31.3659 Å2 / Biso min: 16.34 Å2
Refinement stepCycle: final / Resolution: 1.879→27.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms819 0 25 72 916
Biso mean--40.96 40.49 -
Num. residues----106
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.879-1.92960.24921380.19761221100
1.9296-1.98640.17861290.17331210100
1.9864-2.05050.23511340.16051253100
2.0505-2.12370.20191360.16071260100
2.1237-2.20870.17871360.14631224100
2.2087-2.30920.20061420.15371226100
2.3092-2.43090.18961420.15181241100
2.4309-2.58310.19521400.16531216100
2.5831-2.78240.21711400.15361220100
2.7824-3.0620.18361410.16441235100
3.062-3.50430.19541480.15151221100
3.5043-4.41220.17251400.13441240100
4.4122-27.5740.18911350.1699121799
Refinement TLS params.Method: refined / Origin x: -22.9593 Å / Origin y: 9.7755 Å / Origin z: -5.0076 Å
111213212223313233
T0.2036 Å20.0033 Å2-0.0217 Å2-0.1841 Å20.0015 Å2--0.1776 Å2
L1.6564 °2-0.1956 °20.1283 °2-1.6855 °20.0231 °2--1.0951 °2
S-0.058 Å °-0.0378 Å °0.019 Å °0.1073 Å °0.0245 Å °-0.099 Å °-0.0197 Å °0.0396 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 202
2X-RAY DIFFRACTION1allA321 - 301
3X-RAY DIFFRACTION1allS1 - 72

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