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- PDB-4lru: Crystal structure of glyoxalase III (Orf 19.251) from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 4lru
TitleCrystal structure of glyoxalase III (Orf 19.251) from Candida albicans
ComponentsGlyoxalase III (glutathione-independent)
KeywordsLYASE / DJ-1 superfamily
Function / homology
Function and homology information


D-lactate dehydratase / glyoxalase III activity / yeast-form cell wall / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / fungal biofilm matrix / hyphal cell wall / cytoplasm
Similarity search - Function
: / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Glyoxalase 3
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHasim, S. / Hussin, N.A. / Nickerson, K.W. / Wilson, M.A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: A Glutathione-independent Glyoxalase of the DJ-1 Superfamily Plays an Important Role in Managing Metabolically Generated Methylglyoxal in Candida albicans.
Authors: Hasim, S. / Hussin, N.A. / Alomar, F. / Bidasee, K.R. / Nickerson, K.W. / Wilson, M.A.
History
DepositionJul 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Feb 5, 2014Group: Database references
Revision 1.4Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Glyoxalase III (glutathione-independent)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2423
Polymers26,1211
Non-polymers1212
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.230, 92.230, 59.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Glyoxalase III (glutathione-independent)


Mass: 26121.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Strain: SC5314 / Gene: CaO19.7882, Orf 19.251, orf19.7882 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5AF03, D-lactate dehydratase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 277 K / pH: 4.1
Details: 100 mM sodium acetate pH 4.1, 120 mM ammonium acetate, 27% PEG4000 and 3% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 14, 2011
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→41 Å / Num. obs: 34390 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 51.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RW7

1rw7
PDB Unreleased entry


Resolution: 1.6→41 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.067 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1730 5.1 %RANDOM
Rwork0.158 ---
obs0.159 32486 99.6 %-
all-34216 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 8 279 2130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191965
X-RAY DIFFRACTIONr_bond_other_d00.021849
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.962672
X-RAY DIFFRACTIONr_angle_other_deg0.6334293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0345254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98626.2588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21415334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.712152
X-RAY DIFFRACTIONr_chiral_restr0.0770.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02422
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5031.598996
X-RAY DIFFRACTIONr_mcbond_other1.4781.589994
X-RAY DIFFRACTIONr_mcangle_it2.0042.3861256
X-RAY DIFFRACTIONr_mcangle_other2.0082.3871265
X-RAY DIFFRACTIONr_scbond_it2.3611.843969
X-RAY DIFFRACTIONr_scbond_other2.3631.844974
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3772.6661423
X-RAY DIFFRACTIONr_long_range_B_refined6.34714.9632501
X-RAY DIFFRACTIONr_long_range_B_other6.34614.9782502
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 126 -
Rwork0.234 2354 -
obs--99.52 %
Refinement TLS params.Method: refined / Origin x: 27.371 Å / Origin y: -4.6984 Å / Origin z: 2.1548 Å
111213212223313233
T0.014 Å20 Å2-0.0085 Å2-0.0122 Å20.0043 Å2--0.0073 Å2
L1.63 °20.0223 °20.0286 °2-1.0637 °20.0843 °2--1.7211 °2
S-0.0576 Å °0.0168 Å °0.024 Å °0.0604 Å °0.0896 Å °-0.014 Å °-0.0104 Å °-0.0441 Å °-0.032 Å °

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