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- PDB-1qip: HUMAN GLYOXALASE I COMPLEXED WITH S-P-NITROBENZYLOXYCARBONYLGLUTA... -

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Basic information

Entry
Database: PDB / ID: 1qip
TitleHUMAN GLYOXALASE I COMPLEXED WITH S-P-NITROBENZYLOXYCARBONYLGLUTATHIONE
ComponentsPROTEIN (LACTOYLGLUTATHIONE 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 / 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
BETA-MERCAPTOETHANOL / S-P-NITROBENZYLOXYCARBONYLGLUTATHIONE / Lactoylglutathione lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.72 Å
AuthorsCameron, A.D. / Ridderstrom, M. / Olin, B. / Mannervik, B.
CitationJournal: Biochemistry / Year: 1999
Title: Reaction mechanism of glyoxalase I explored by an X-ray crystallographic analysis of the human enzyme in complex with a transition state analogue.
Authors: Cameron, A.D. / Ridderstrom, M. / Olin, B. / Kavarana, M.J. / Creighton, D.J. / Mannervik, B.
History
DepositionJun 14, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 24, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_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.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: PROTEIN (LACTOYLGLUTATHIONE LYASE)
B: PROTEIN (LACTOYLGLUTATHIONE LYASE)
C: PROTEIN (LACTOYLGLUTATHIONE LYASE)
D: PROTEIN (LACTOYLGLUTATHIONE LYASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,21816
Polymers82,6904
Non-polymers2,52812
Water16,304905
1
A: PROTEIN (LACTOYLGLUTATHIONE LYASE)
B: PROTEIN (LACTOYLGLUTATHIONE LYASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6098
Polymers41,3452
Non-polymers1,2646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-146 kcal/mol
Surface area15830 Å2
MethodPISA, PQS
2
C: PROTEIN (LACTOYLGLUTATHIONE LYASE)
D: PROTEIN (LACTOYLGLUTATHIONE LYASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6098
Polymers41,3452
Non-polymers1,2646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10270 Å2
ΔGint-147 kcal/mol
Surface area16090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.300, 67.300, 167.700
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(-0.79932, 0.35493, 0.48488), (0.35423, -0.37348, 0.85734), (0.48539, 0.85705, 0.1728)96.10732, 20.19166, -54.46898
2given(-0.00456, 0.99999, -0.00079), (0.99898, 0.00459, 0.04503), (0.04503, -0.00059, -0.99899)34.09876, -15.8381, 33.82902
3given(0.35238, -0.38241, 0.85416), (-0.77669, 0.38968, 0.49488), (-0.5221, -0.8378, -0.15969)54.35896, 77.82969, 92.54097

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Components

#1: Protein
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) / Description: HETEROLOGOUSLY EXPRESSED / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM 103 / 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-GNB / S-P-NITROBENZYLOXYCARBONYLGLUTATHIONE


Mass: 488.469 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H24N4O10S
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 905 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOVALENTLY LINKED TO CYS 60
Sequence detailsREFERENCE FOR THE SEQUENCE DATABASE: M.RIDDERSTROM, B.MANNERVIK, BIOCHEM J. 314, 463-467, 1996.

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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: 40 %
Crystal growpH: 5.8
Details: PROTEIN WAS CRYSTALLISED BY EQILLABRATION AGAINST PEG 2000 MONOMETHLY ETHER, 50 MM MES PH 5.8, 0.1M NACL THEN SOAKED IN 10MM NBC-GSH
Crystal
*PLUS
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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9123
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 8, 1996 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATORN / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9123 Å / Relative weight: 1
ReflectionResolution: 1.72→28 Å / Num. obs: 78648 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 4.1 / % possible all: 100
Reflection
*PLUS
Num. measured all: 311697
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.72→30 Å / SU B: 2.1 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.11
Details: THE 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. DISORDERED SIDE ...Details: THE 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. DISORDERED SIDE CHAINS HAVE BEEN INCLUDED WITH OCCUPANCIES OF 0.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2264 3 %SHELLS
Rwork0.18 ---
obs0.17 78648 100 %-
Displacement parametersBiso mean: 25 Å2
Refinement stepCycle: LAST / Resolution: 1.72→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5699 0 152 905 6756
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0230.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0240.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9422
X-RAY DIFFRACTIONp_mcangle_it1.4512.5
X-RAY DIFFRACTIONp_scbond_it2.5294
X-RAY DIFFRACTIONp_scangle_it3.5516
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.10.15
X-RAY DIFFRACTIONp_singtor_nbd0.1710.3
X-RAY DIFFRACTIONp_multtor_nbd0.2320.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.67
X-RAY DIFFRACTIONp_staggered_tor14.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor35.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.17 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.10.15

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