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- PDB-4opn: Crystal structure of mouse glyoxalase I complexed with mAH -

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Basic information

Entry
Database: PDB / ID: 4opn
TitleCrystal structure of mouse glyoxalase I complexed with mAH
ComponentsLactoylglutathione lyase
KeywordsLYASE/LYASE INHIBITOR / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


Pyruvate metabolism / lactoylglutathione lyase / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / lactoylglutathione lyase activity / methylglyoxal metabolic process / glutathione metabolic process / osteoclast differentiation / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / zinc ion binding ...Pyruvate metabolism / lactoylglutathione lyase / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / lactoylglutathione lyase activity / methylglyoxal metabolic process / glutathione metabolic process / osteoclast differentiation / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / plasma membrane / cytosol
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
Chem-ZBF / Lactoylglutathione lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhai, J. / Zhang, L. / Yuan, M. / Zhang, H.
CitationJournal: To be Published
Title: Reversible Inhibition of Glyoxalase I: Synthesis and Activity Evaluation
Authors: Shi, Q. / Zhai, J. / Zheng, Z. / Hu, X.
History
DepositionFeb 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Lactoylglutathione lyase
B: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6996
Polymers41,6712
Non-polymers1,0284
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-130 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.559, 65.084, 64.885
Angle α, β, γ (deg.)90.00, 101.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lactoylglutathione lyase / Glyoxalase I / Aldoketomutase / Glx I / Ketone-aldehyde mutase / Methylglyoxalase / S-D- ...Glyoxalase I / Aldoketomutase / Glx I / Ketone-aldehyde mutase / Methylglyoxalase / S-D-lactoylglutathione methylglyoxal lyase


Mass: 20835.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Glo1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(+) / References: UniProt: Q9CPU0, lactoylglutathione lyase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ZBF / L-gamma-glutamyl-N-(3-ethynylphenyl)-N-hydroxy-L-glutaminylglycine


Mass: 448.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N4O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 30% PEG 2000, 50mM MES, 0.1M NaCl, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Mar 15, 2012
RadiationMonochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25.615 Å / Num. all: 19556 / Num. obs: 19556 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 22.71 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.1001-2.2107195.92
2.2107-25.6167198.2

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Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25.615 Å / FOM work R set: 0.8445 / SU ML: 0.21 / σ(F): 1.36 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 1001 5.12 %RANDOM
Rwork0.177 18555 --
obs0.1798 19556 98.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.27 Å2 / Biso mean: 27.05 Å2 / Biso min: 10.49 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 66 276 3084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082886
X-RAY DIFFRACTIONf_angle_d1.0113909
X-RAY DIFFRACTIONf_chiral_restr0.037414
X-RAY DIFFRACTIONf_plane_restr0.005526
X-RAY DIFFRACTIONf_dihedral_angle_d12.6061085
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.21070.27111380.21222669280799
2.2107-2.34920.26141330.216926932826100
2.3492-2.53040.29461360.207226662802100
2.5304-2.78480.24361360.20762703283999
2.7848-3.18710.2571500.18742658280899
3.1871-4.01290.21641540.15432608276297
4.0129-25.61670.18761540.14362558271293

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