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- PDB-1bh5: HUMAN GLYOXALASE I Q33E, E172Q DOUBLE MUTANT -

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Basic information

Entry
Database: PDB / ID: 1bh5
TitleHUMAN GLYOXALASE I Q33E, E172Q DOUBLE MUTANT
ComponentsLACTOYLGLUTATHIONE LYASE
KeywordsLYASE / LACTOYLGLUTATHIONE 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 / 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
S-HEXYLGLUTATHIONE / Lactoylglutathione lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.2 Å
AuthorsCameron, A.D. / Jones, T.A.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Involvement of an active-site Zn2+ ligand in the catalytic mechanism of human glyoxalase I.
Authors: Ridderstrom, M. / Cameron, A.D. / Jones, T.A. / Mannervik, B.
History
DepositionJun 13, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)84,52212
Polymers82,6904
Non-polymers1,8328
Water9,134507
1
A: LACTOYLGLUTATHIONE LYASE
B: LACTOYLGLUTATHIONE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2616
Polymers41,3452
Non-polymers9164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-149 kcal/mol
Surface area16060 Å2
MethodPISA
2
C: LACTOYLGLUTATHIONE LYASE
D: LACTOYLGLUTATHIONE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2616
Polymers41,3452
Non-polymers9164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-150 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.280, 67.280, 164.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.37034, 0.39138, 0.84242), (0.38185, -0.76259, 0.52216), (0.84678, 0.51506, 0.13296)-98.04543, -48.25381, 95.26162
2given(0.99999, -0.00353, 0.00262), (-0.00352, -0.99997, -0.007), (0.00264, 0.00699, -0.99997)33.38152, -12.60521, 244.40053
3given(-0.36765, 0.3974, 0.84078), (-0.38877, 0.75563, -0.52715), (-0.8448, -0.52067, -0.12331)-64.24339, 35.45904, 148.06689
DetailsTHE BIOLOGICALLY ACTIVE MOLECULE IS THE DIMER (MOLECULES A AND B OR C AND D). THE TWO DIMERS IN THE ASYMMETRIC UNIT ARE SITUATED IN SIMILAR CRYSTALLOGRAHIC ENVIRONMENTS. DURING REFINEMENT NON-CRYSTALLOGRAPHIC RESTRAINTS WERE APPLIED BETWEEN THE A AND C MOLECULES AND BETWEEN THE B AND D MOLECULES). NO NCS RESTRAINTS WERE APPLIED BETWEEN THE TWO MOLECULES OF THE DIMERS. DISORDERED SIDE CHAINS HAVE BEEN INCLUDED WITH OCCUPANCIES OF 0.01. RESIDUE CYS 60 IN THE B AND D MOLECULES APPEARS TO BE INVOLVED IN A DISULFIDE BRIDGE WITH 2-MERCAPTOETHANOL AS STATED FOR 1FRO.PDB. THE 2-MERCAPTOETHANOL HAS NOT BEEN MODELLED DUE TO THE LIMITED NUMBER OF DATA.

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Components

#1: Protein
LACTOYLGLUTATHIONE LYASE / / GLYOXALASE I


Mass: 20672.520 Da / Num. of mol.: 4 / Mutation: Q33E, E172Q
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-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H30N3O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 507 / 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 Å3/Da / Density % sol: 42 %
Crystal growpH: 5.8
Details: PROTEIN WAS CRYSTALLISED FROM PEG 2000 MONOMETHLY ETHER 50 MM MES PH 5.8, 0.1M NACL
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion, hanging drop / Details: Cameron, A.D., (1997) EMBO J., 16, 3386.
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: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 23, 1997
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: 33195 / % possible obs: 89.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 27
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 5.5 / % possible all: 63.1
Reflection shell
*PLUS
% possible obs: 63 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 1FRO

1fro


Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1679 5 %RANDOM
Rwork0.18 ---
obs0.19 33193 89.7 %-
Displacement parametersBiso mean: 16 Å2
Refine analyzeLuzzati sigma a obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5702 0 108 507 6317
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0352
X-RAY DIFFRACTIONp_mcangle_it1.5252.5
X-RAY DIFFRACTIONp_scbond_it3.0364
X-RAY DIFFRACTIONp_scangle_it3.7726
X-RAY DIFFRACTIONp_plane_restr0.021
X-RAY DIFFRACTIONp_chiral_restr0.1080.15
X-RAY DIFFRACTIONp_singtor_nbd0.1770.3
X-RAY DIFFRACTIONp_multtor_nbd0.2330.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1790.3
X-RAY DIFFRACTIONp_planar_tor3.77
X-RAY DIFFRACTIONp_staggered_tor17.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor35.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.25 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS

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