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- PDB-6bnx: Crystal structure of V278E-glyoxalase I mutant from Zea mays in s... -

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Basic information

Entry
Database: PDB / ID: 6bnx
TitleCrystal structure of V278E-glyoxalase I mutant from Zea mays in space group P6(3)
ComponentsLactoylglutathione lyase
KeywordsPLANT PROTEIN / PLANT PROTEIN defense
Function / homology
Function and homology information


lactoylglutathione lyase / lactoylglutathione lyase activity / metal ion binding
Similarity search - Function
Glyoxalase I signature 2. / Glyoxalase I / Glyoxalase I, conserved site / Glyoxalase I signature 1. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. ...Glyoxalase I signature 2. / Glyoxalase I / Glyoxalase I, conserved site / Glyoxalase I signature 1. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / Lactoylglutathione lyase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAlvarez, C.E. / Agostini, R.B. / Gonzalez, J.M. / Drincovich, M.F. / Campos Bermudez, V.A. / Klinke, S.
CitationJournal: Febs J. / Year: 2019
Title: Deciphering the number and location of active sites in the monomeric glyoxalase I of Zea mays.
Authors: Gonzalez, J.M. / Agostini, R.B. / Alvarez, C.E. / Klinke, S. / Andreo, C.S. / Campos-Bermudez, V.A.
History
DepositionNov 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0482
Polymers32,9891
Non-polymers591
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.110, 82.110, 74.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Lactoylglutathione lyase / Glyoxalase I


Mass: 32989.395 Da / Num. of mol.: 1 / Fragment: residues 26-315 / Mutation: V278E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Plasmid: pET 28b / Details (production host): resistance to kanamycin / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: B6TPH0, lactoylglutathione lyase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.25 Å3/Da / Density % sol: 45.35 % / Description: needle bunch
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9.7 / Details: sodium formate 4.2 M pH 9.7, 0.5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 11, 2016 / Details: Kirkpatrick-Baez pair of bi-morph mirrors
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.8→41.06 Å / Num. obs: 26692 / % possible obs: 99.9 % / Redundancy: 10.27 % / CC1/2: 1 / Rrim(I) all: 0.067 / Net I/σ(I): 19.7
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 10.32 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4293 / CC1/2: 0.666 / Rrim(I) all: 1.375 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D7Z

5d7z


Resolution: 1.8→41.05 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.8 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.126
RfactorNum. reflection% reflectionSelection details
Rfree0.22406 1335 5 %RANDOM
Rwork0.18346 ---
obs0.1855 25355 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.629 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.36 Å2-0 Å2
2--0.72 Å20 Å2
3----2.32 Å2
Refinement stepCycle: 1 / Resolution: 1.8→41.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2222 0 1 154 2377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192277
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.9723080
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9985282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.18824.476105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06415397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9721511
X-RAY DIFFRACTIONr_chiral_restr0.1220.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211730
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.0343.6281125
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.3415.4181405
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0333.9441152
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.44649.0653434
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.508 96 -
Rwork0.503 1832 -
obs--98.87 %

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