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- PDB-3w0t: Human Glyoxalase I with an N-hydroxypyridone derivative inhibitor -

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Basic information

Entry
Database: PDB / ID: 3w0t
TitleHuman Glyoxalase I with an N-hydroxypyridone derivative inhibitor
ComponentsLactoylglutathione lyase
KeywordsLYASE/LYASE INHIBITOR / Glyoxalase / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal metabolic process / Pyruvate metabolism / glutathione metabolic process / osteoclast differentiation / carbohydrate metabolic process / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / extracellular exosome ...lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal metabolic process / Pyruvate metabolism / glutathione metabolic process / osteoclast differentiation / carbohydrate metabolic process / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / extracellular exosome / zinc ion binding / nucleoplasm / plasma membrane / cytosol / cytoplasm
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-HPU / Lactoylglutathione lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.351 Å
AuthorsFukami, T.A. / Irie, M. / Matsuura, T.
CitationJournal: To be Published
Title: N-Hydroxypyridone-based glyoxalase I inhibitors mimicking binding interactions of the substrate
Authors: Koyano, H. / Aoki, T. / Yamamoto, S. / Kobayashi, T. / Miura, T. / Ohara, K. / Fukami, T.A. / Irie, M. / Sakamoto, H.
History
DepositionNov 2, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_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: Lactoylglutathione lyase
B: Lactoylglutathione lyase
C: Lactoylglutathione lyase
D: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,74615
Polymers84,3444
Non-polymers2,40211
Water17,276959
1
A: Lactoylglutathione lyase
B: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4928
Polymers42,1722
Non-polymers1,3206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-136 kcal/mol
Surface area15970 Å2
MethodPISA
2
C: Lactoylglutathione lyase
D: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2547
Polymers42,1722
Non-polymers1,0825
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-135 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.570, 81.030, 68.620
Angle α, β, γ (deg.)90.000, 90.130, 90.000
Int Tables number4
Space group name H-MP1211

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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: 21085.990 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLO1 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04760, lactoylglutathione lyase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-HPU / N-[3-(1-hydroxy-6-oxo-4-phenyl-1,6-dihydropyridin-2-yl)phenyl]methanesulfonamide


Mass: 356.396 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H16N2O4S
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 959 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 33% (w/v) PEG 2000 MME, 0.1M Na-HEPES (pH 7.0), vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 20, 2009 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.351→23.507 Å / Num. all: 145439 / Num. obs: 145439 / % possible obs: 91.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.93 Å2 / Rsym value: 0.048 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.35-1.392.30.9570.7251.11541265930.6150.9570.7251.356.2
1.39-1.422.60.7920.6171.21951476430.4860.7920.6171.667.2
1.42-1.472.80.6220.4971.62433487450.3670.6220.4972.279
1.47-1.513.10.480.3961.931614100580.2660.480.396393.1
1.51-1.563.70.3990.3412.337937102900.2050.3990.341498.2
1.56-1.613.70.310.2652.93667399210.1590.310.265598.4
1.61-1.683.70.240.2053.83564296690.1230.240.2056.398.5
1.68-1.743.70.1880.164.83423592750.0970.1880.167.898.8
1.74-1.823.70.1480.1276.13284888950.0760.1480.1279.598.9
1.82-1.913.70.1060.098.43162185750.0550.1060.0912.798.9
1.91-2.013.70.0810.06910.82991981100.0420.0810.06915.698.8
2.01-2.143.70.0640.05413.22835076980.0330.0640.05418.998.9
2.14-2.283.70.0550.047152673372540.0280.0550.04721.499.1
2.28-2.473.70.0490.042162506267650.0250.0490.04223.499.2
2.47-2.73.70.0450.039172303562090.0230.0450.03925.499.3
2.7-3.023.70.040.03418.52081256110.020.040.03427.898.8
3.02-3.493.70.0370.03219.21839749830.0190.0370.03230.398.7
3.49-4.273.70.0330.02821.71534541790.0170.0330.0283298.5
4.27-6.043.60.0320.02821.31166732260.0170.0320.02832.397.6
6.04-23.5073.40.040.03317.7594717400.0210.040.03331.394

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.42
Highest resolutionLowest resolution
Rotation2.5 Å23.51 Å
Translation2.5 Å23.51 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VW9

3vw9


Resolution: 1.351→19.77 Å / Cor.coef. Fo:Fc: 0.9621 / Cor.coef. Fo:Fc free: 0.9523 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.061 / SU Rfree Blow DPI: 0.061 / SU Rfree Cruickshank DPI: 0.059
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 7284 5.01 %RANDOM
Rwork0.175 ---
obs0.1761 145392 91.18 %-
Displacement parametersBiso max: 92.95 Å2 / Biso mean: 21.9248 Å2 / Biso min: 8.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.3338 Å20 Å2-1.5381 Å2
2---3.3685 Å20 Å2
3---2.0347 Å2
Refine analyzeLuzzati coordinate error obs: 0.155 Å
Refinement stepCycle: LAST / Resolution: 1.351→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5620 0 149 959 6728
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2115SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes161HARMONIC2
X-RAY DIFFRACTIONt_gen_planes845HARMONIC5
X-RAY DIFFRACTIONt_it5981HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion748SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7600SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5981HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8109HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion4.13
X-RAY DIFFRACTIONt_other_torsion16.32
LS refinement shellResolution: 1.35→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 307 4.8 %
Rwork0.2409 6092 -
all0.2417 6399 -
obs--91.18 %

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