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- PDB-7dit: Structure of PfGrx1 in the intermediate state with cadmium and cesium -

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Basic information

Entry
Database: PDB / ID: 7dit
TitleStructure of PfGrx1 in the intermediate state with cadmium and cesium
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / REDOX ENZYME / TRX FOLD / GLUTATHIONE / Cd-SAD / CSO / S-HYDROXYCYSTEINE
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
: / : / Glutaredoxin-1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SAD / 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 13, 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)13,90314
Polymers12,4521
Non-polymers1,45113
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-24 kcal/mol
Surface area5850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.435, 48.435, 82.737
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: 12452.457 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 , 6 types, 139 molecules

#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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.33 %
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 4, 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: 10913 / % possible obs: 99.9 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.065 / Χ2: 1.357 / Net I/σ(I): 12.9 / Num. measured all: 158175
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.8314.20.5455071.0011100
1.83-1.8614.60.4455541.011100
1.86-1.914.20.3725211.0561100
1.9-1.9414.60.355511.061100
1.94-1.9814.40.2775061.0891100
1.98-2.0314.60.2345541.11100
2.03-2.0814.50.1985271.1361100
2.08-2.1314.50.1765421.2451100
2.13-2.214.80.1435391.1561100
2.2-2.2714.50.1245481.2161100
2.27-2.3514.70.115271.2741100
2.35-2.4414.70.0935441.2741100
2.44-2.5514.90.0935441.3661100
2.55-2.6914.70.0795491.3861100
2.69-2.8614.80.0695411.5111100
2.86-3.0814.70.0555471.5951100
3.08-3.3914.80.0465571.71100
3.39-3.8814.50.0395661.8431100
3.88-4.8814.30.0365751.9251100
4.88-5013.10.0416142.075198.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
Auto-Rickshawphasing
SHELXDEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→24.218 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 524 4.81 %
Rwork0.1674 10360 -
obs0.1691 10884 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.79 Å2 / Biso mean: 25.5247 Å2 / Biso min: 12.23 Å2
Refinement stepCycle: final / Resolution: 1.8→24.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 32 128 978
Biso mean--36.3 37.72 -
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
1.8-1.98070.23071430.17762494
1.9807-2.26710.22731200.15742577
2.2671-2.85560.21131330.17682575
2.8556-24.2180.18241280.16442714
Refinement TLS params.Method: refined / Origin x: -23.1399 Å / Origin y: 9.959 Å / Origin z: -4.8097 Å
111213212223313233
T0.1585 Å2-0.0107 Å2-0.0025 Å2-0.1515 Å20.0048 Å2--0.1374 Å2
L2.4975 °2-1.0128 °20.6394 °2-3.0701 °2-0.3023 °2--1.6353 °2
S-0.064 Å °-0.036 Å °0.0725 Å °0.1125 Å °0.0083 Å °-0.0681 Å °-0.0225 Å °0.0272 Å °0.0004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 202
2X-RAY DIFFRACTION1allA301 - 402
3X-RAY DIFFRACTION1allS1 - 126

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