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- PDB-4mzc: Atomic Resolution Structure of PfGrx1 -

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Basic information

Entry
Database: PDB / ID: 4mzc
TitleAtomic Resolution Structure of PfGrx1
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / glutathione / sulfur-SAD / active site / plasticity / TRX fold / redox enzyme
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.949 Å
AuthorsYogavel, M. / Sharma, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Atomic resolution crystal structure of glutaredoxin 1 from Plasmodium falciparum and comparison with other glutaredoxins.
Authors: Yogavel, M. / Tripathi, T. / Gupta, A. / Banday, M.M. / Rahlfs, S. / Becker, K. / Belrhali, H. / Sharma, A.
History
DepositionSep 30, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionOct 9, 2013ID: 4KJF
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.971, 47.971, 82.473
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 (malaria parasite P. falciparum)
Strain: 3D7 / Gene: GRX1, PFC0271c / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q9NLB2, arsenate reductase (glutathione/glutaredoxin)
#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.: 164 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.16 %
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, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.72932 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2012 / Details: mirrors
RadiationMonochromator: Si(III) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72932 Å / Relative weight: 1
ReflectionResolution: 0.949→50 Å / Num. all: 70202 / Num. obs: 69290 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 21 % / Biso Wilson estimate: 7.85 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 43.02
Reflection shellResolution: 0.949→0.97 Å / Redundancy: 21.5 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 6.7 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HJM

4hjm


Resolution: 0.949→23.985 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.9617 / SU ML: 0.05 / σ(F): 1.34 / Phase error: 7.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1109 3499 5.05 %RANDOM
Rwork0.1039 ---
obs0.1042 69221 98.7 %-
all-69290 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.55 Å2 / Biso mean: 13.3007 Å2 / Biso min: 4.59 Å2
Refinement stepCycle: LAST / Resolution: 0.949→23.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 21 164 1017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011040
X-RAY DIFFRACTIONf_angle_d1.4751421
X-RAY DIFFRACTIONf_chiral_restr0.076157
X-RAY DIFFRACTIONf_plane_restr0.006184
X-RAY DIFFRACTIONf_dihedral_angle_d13.25446
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.949-0.9620.14351530.11572608276199
0.962-0.97580.1231460.105726452791100
0.9758-0.99030.11211350.100926112746100
0.9903-1.00580.11361380.095626282766100
1.0058-1.02230.09721190.087426772796100
1.0223-1.03990.11311300.08226302760100
1.0399-1.05880.08541480.080326112759100
1.0588-1.07920.0741340.074826182752100
1.0792-1.10120.08641490.07526642813100
1.1012-1.12520.08321310.074326442775100
1.1252-1.15130.07211310.070426252756100
1.1513-1.18010.06671270.07126602787100
1.1801-1.2120.09291600.073926212781100
1.212-1.24770.08591550.079826342789100
1.2477-1.2880.0831280.080126692797100
1.288-1.3340.09951470.084726572804100
1.334-1.38740.09351380.085626502788100
1.3874-1.45050.11031610.08826522813100
1.4505-1.5270.10091550.087726422797100
1.527-1.62260.09491450.092226742819100
1.6226-1.74790.11131290.098526962825100
1.7479-1.92370.11311320.105727202852100
1.9237-2.20190.12091520.10726882840100
2.2019-2.77350.12461460.11882729287599
2.7735-23.99320.15321100.17112069217972

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