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- PDB-7vq6: Structure of a specialized glyoxalase from Gossypium hirsutum -

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Basic information

Entry
Database: PDB / ID: 7vq6
TitleStructure of a specialized glyoxalase from Gossypium hirsutum
ComponentsLactoylglutathione lyase
KeywordsLYASE / glyoxalase
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. / 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
Similarity search - Domain/homology
NICKEL (II) ION / Lactoylglutathione lyase
Similarity search - Component
Biological speciesGossypium hirsutum (cotton)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsLi, H. / Hu, Y.M. / Dai, L.H. / Chen, C.C. / Huang, J.W. / Liu, W.D. / Guo, R.T.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Crystal structure and biochemical analysis of the specialized deoxynivalenol-detoxifying glyoxalase SPG from Gossypium hirsutum.
Authors: Hu, Y. / Li, H. / Min, J. / Yu, Y. / Liu, W. / Huang, J.W. / Zhang, L. / Yang, Y. / Dai, L. / Chen, C.C. / Guo, R.T.
History
DepositionOct 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactoylglutathione lyase
B: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7044
Polymers42,5862
Non-polymers1172
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-59 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.255, 49.507, 58.413
Angle α, β, γ (deg.)90.000, 99.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lactoylglutathione lyase / Glyoxalase I


Mass: 21293.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gossypium hirsutum (cotton) / Gene: LOC107963917 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1U8Q028, lactoylglutathione lyase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: MgAC; Sodium Cacodylate ; PEG 4000.

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Sep 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 1.39→44.48 Å / Num. obs: 66039 / % possible obs: 99.8 % / Redundancy: 6.85 % / Rmerge(I) obs: 0.0809 / Net I/σ(I): 12.8
Reflection shellResolution: 1.39→1.49 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 2731

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Cootmodel building
SAINTdata reduction
SADABSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QIP

1qip


Resolution: 1.39→44.48 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.636 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.012 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.186 3338 5.1 %RANDOM
Rwork0.157 ---
obs0.159 62340 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.72 Å2 / Biso mean: 13.291 Å2 / Biso min: 4.52 Å2
Baniso -1Baniso -2Baniso -3
1-5.86 Å20 Å2-0.8 Å2
2---4.13 Å2-0 Å2
3----1.73 Å2
Refinement stepCycle: final / Resolution: 1.39→44.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 2 472 3223
Biso mean--30 25.62 -
Num. residues----343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132964
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172662
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.6584031
X-RAY DIFFRACTIONr_angle_other_deg1.5841.5786230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8645368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01923.007153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68215511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5421514
X-RAY DIFFRACTIONr_chiral_restr0.1140.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023359
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02631
LS refinement shellResolution: 1.39→1.426 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 225 -
Rwork0.227 4421 -
all-4646 -
obs--96.41 %

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