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- PDB-6l0u: Crystal structure of mouse glyoxalase I complexed with a small mo... -

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Basic information

Entry
Database: PDB / ID: 6l0u
TitleCrystal structure of mouse glyoxalase I complexed with a small molecule inhibitor
ComponentsLactoylglutathione lyase
KeywordsLYASE/LYASE INHIBITOR / mouse glyoxalase I / inhibitor / LYASE / 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 / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / 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 / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / zinc ion binding / nucleoplasm / plasma membrane / cytosol
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
Chem-E1L / Lactoylglutathione lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsJiang, L.L. / Zhou, L.
CitationJournal: To Be Published
Title: Crystal structure of mouse glyoxalase I complexed with a small molecule inhibitor
Authors: Jiang, L.L. / Zhou, L.
History
DepositionSep 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)41,0805
Polymers40,5582
Non-polymers5223
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-129 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.785, 64.635, 65.794
Angle α, β, γ (deg.)90.000, 101.580, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ILE / End label comp-ID: ILE

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROPROchain AAA6 - 1841 - 179
2SERSERchain BBB8 - 1843 - 179

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Components

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


Mass: 20278.953 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) / 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-E1L / N-[4-(trifluoromethyloxy)phenyl]-1,3,4,9-tetrahydropyrido[3,4-b]indole-2-carbothioamide


Mass: 391.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16F3N3OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES pH 6.0, 12% (w/v) PEG2000, 16% v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 25098 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Χ2: 0.663 / Net I/σ(I): 5.3 / Num. measured all: 167399
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.95-2.026.20.57225070.8640.2460.6240.433
2.02-2.16.30.43224780.9220.1850.470.469
2.1-2.26.90.31825210.9530.1290.3440.505
2.2-2.316.90.24424780.9690.0990.2640.53
2.31-2.466.50.1825110.9810.0760.1960.576
2.46-2.656.70.14324910.9870.060.1550.629
2.65-2.9170.10324880.9940.0410.1110.74
2.91-3.336.50.07325100.9950.0310.080.872
3.33-4.270.05325340.9980.0210.0570.991
4.2-506.50.04125800.9990.0170.0440.84

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZA0

2za0


Resolution: 1.95→23.16 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.46
RfactorNum. reflection% reflection
Rfree0.2443 1277 5.1 %
Rwork0.1965 --
obs0.1989 25062 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.82 Å2 / Biso mean: 41.79 Å2 / Biso min: 18.66 Å2
Refinement stepCycle: final / Resolution: 1.95→23.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 45 108 2987
Biso mean--56.09 40.12 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082935
X-RAY DIFFRACTIONf_angle_d1.2473974
X-RAY DIFFRACTIONf_chiral_restr0.088424
X-RAY DIFFRACTIONf_plane_restr0.007509
X-RAY DIFFRACTIONf_dihedral_angle_d14.1051093
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1646X-RAY DIFFRACTION8.628TORSIONAL
12B1646X-RAY DIFFRACTION8.628TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-2.02880.30661490.2449258298
2.0288-2.1210.26781360.23192648100
2.121-2.23280.2471160.21272650100
2.2328-2.37250.26041280.2142639100
2.3725-2.55550.2661600.21182615100
2.5555-2.81230.27031450.21392660100
2.8123-3.21830.24111530.19422638100
3.2183-4.05120.24511410.18632653100
4.0512-23.160.22141490.18232700100

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