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- PDB-4hjm: Crystal structure of Glutaredoxin 1 from Plasmodium falciparum (P... -

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Basic information

Entry
Database: PDB / ID: 4hjm
TitleCrystal structure of Glutaredoxin 1 from Plasmodium falciparum (PfGrx1) solved by S-SAD
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / glutathione / sulfur-SAD / active site / plasticity / Trx fold / redox enzymes
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 / SAD / Resolution: 1.5462 Å
AuthorsManickam, Y. / 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
DepositionOct 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.092, 48.092, 82.594
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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.: 171 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 19, 2011
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5462→50 Å / Num. all: 16595 / Num. obs: 16572 / % possible obs: 99.01 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 19 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 91.2
Reflection shellResolution: 1.5462→1.6 Å / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 13.2 / % possible all: 83.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5462→24.046 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.11 / SU R Cruickshank DPI: 0.0775 / σ(F): 1.36 / Phase error: 16.56 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rfree0.1787 839 5.06 %
Rwork0.148 --
obs0.1495 16568 99.05 %
all-16595 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.5799 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.5462→24.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 20 171 1023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006963
X-RAY DIFFRACTIONf_angle_d1.0931309
X-RAY DIFFRACTIONf_dihedral_angle_d13.815408
X-RAY DIFFRACTIONf_chiral_restr0.073147
X-RAY DIFFRACTIONf_plane_restr0.004166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5462-1.64310.20331260.16662506X-RAY DIFFRACTION97
1.6431-1.76990.17981670.15652549X-RAY DIFFRACTION99
1.7699-1.94790.20681320.14392590X-RAY DIFFRACTION99
1.9479-2.22960.18421430.14092620X-RAY DIFFRACTION100
2.2296-2.80840.17051310.14982677X-RAY DIFFRACTION100
2.8084-24.04890.17091400.14712787X-RAY DIFFRACTION100

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