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- PDB-1fro: HUMAN GLYOXALASE I WITH BENZYL-GLUTATHIONE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1fro
TitleHUMAN GLYOXALASE I WITH BENZYL-GLUTATHIONE INHIBITOR
ComponentsLACTOYLGLUTATHIONE LYASE
KeywordsLACTOYLGLUTATHIONE LYASE / GLYOXALASE I
Function / homology
Function and homology information


lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal metabolic process / Pyruvate metabolism / glutathione metabolic process / osteoclast differentiation / carbohydrate metabolic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / extracellular exosome ...lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal metabolic process / Pyruvate metabolism / glutathione metabolic process / osteoclast differentiation / carbohydrate metabolic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / extracellular exosome / zinc ion binding / nucleoplasm / plasma membrane / cytoplasm / 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
S-BENZYL-GLUTATHIONE / Lactoylglutathione lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsCameron, A.D. / Jones, T.A.
CitationJournal: EMBO J. / Year: 1997
Title: Crystal structure of human glyoxalase I--evidence for gene duplication and 3D domain swapping.
Authors: Cameron, A.D. / Olin, B. / Ridderstrom, M. / Mannervik, B. / Jones, T.A.
History
DepositionFeb 25, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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
C: LACTOYLGLUTATHIONE LYASE
D: LACTOYLGLUTATHIONE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,54212
Polymers82,6904
Non-polymers1,8518
Water6,485360
1
A: LACTOYLGLUTATHIONE LYASE
B: LACTOYLGLUTATHIONE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2716
Polymers41,3452
Non-polymers9264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9500 Å2
ΔGint-137 kcal/mol
Surface area15230 Å2
MethodPISA
2
C: LACTOYLGLUTATHIONE LYASE
D: LACTOYLGLUTATHIONE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2716
Polymers41,3452
Non-polymers9264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-136 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.000, 68.000, 169.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.815136, 0.343255, 0.466615), (0.344742, -0.359879, 0.866972), (0.465517, 0.867562, 0.175016)98.24847, 20.39418, -54.03745
2given(-0.007761, 0.999943, -0.007301), (0.99907, 0.008064, 0.042358), (0.042414, -0.006966, -0.999076)34.42899, -16.08493, 34.15934
3given(0.347653, -0.368774, 0.862058), (-0.791885, 0.376816, 0.480549), (-0.502051, -0.849715, -0.161026)54.45139, 79.94658, 92.17197

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Components

#1: Protein
LACTOYLGLUTATHIONE LYASE / GLYOXALASE I


Mass: 20672.520 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / 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-GSB / S-BENZYL-GLUTATHIONE


Mass: 397.446 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H23N3O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.37 Å3/Da / Density % sol: 42 %
Crystal growpH: 5.8 / Details: pH 5.8
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112.5-15 %(w/v)PEG20001drop
225 mMMES1drop
30.05 M1dropNaCl
46 mg/mlprotein1drop
50.5 %2-mercaptoethanol1drop
61 mMS-benzyl-glutathione1drop
725-30 %(w/v)PEG20001reservoir
850 mMMES1reservoir
90.1 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 20, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 35503 / % possible obs: 91.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3 / % possible all: 78.1
Reflection
*PLUS
Num. measured all: 118633
Reflection shell
*PLUS
% possible obs: 79.1 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→7.5 Å / Isotropic thermal model: RESTRAINED INDIVIDUAL
Details: THIS STRUCTURE WAS REFINED WITH STRICT NON-CRYSTALLOGRAPHIC SYMMETRY CONSTRAINTS BETWEEN ALL MOLECULES. WATER MOLECULES B 246 AND B 253 ARE INVOLVED IN STEREOCHEMICAL CLASHES ON GENERATION ...Details: THIS STRUCTURE WAS REFINED WITH STRICT NON-CRYSTALLOGRAPHIC SYMMETRY CONSTRAINTS BETWEEN ALL MOLECULES. WATER MOLECULES B 246 AND B 253 ARE INVOLVED IN STEREOCHEMICAL CLASHES ON GENERATION OF THE FULL ASYMMETRIC UNIT. DISORDERED SIDE CHAINS HAVE BEEN INCLUDED WITH OCCUPANCIES OF 0.01. THE DENSITY ASSOCIATED WITH THE LAST THREE RESIDUES IS RATHER POOR AND CONSEQUENTLY THE POSITIONS OF THESE RESIDUES ARE RATHER AMBIGUOUS.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1785 5 %NARROW SPHERES
Rwork0.211 ---
obs0.211 34555 --
Displacement parametersBiso mean: 23.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1400 0 27 90 1517
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.52
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.26
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it21.5
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it2.52
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: STRICT NCS
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.233 238 5 %
Rwork0.273 3477 -
obs--79 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.26

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