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- PDB-1qin: HUMAN GLYOXALASE I COMPLEXED WITH S-(N-HYDROXY-N-P-IODOPHENYLCARB... -

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Basic information

Entry
Database: PDB / ID: 1qin
TitleHUMAN GLYOXALASE I COMPLEXED WITH S-(N-HYDROXY-N-P-IODOPHENYLCARBAMOYL) GLUTATHIONE
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 / 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-(N-HYDROXY-N-IODOPHENYLCARBAMOYL)GLUTATHIONE / Lactoylglutathione lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2 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 / 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.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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6176
Polymers41,3452
Non-polymers1,2724
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-150 kcal/mol
Surface area15310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.700, 54.500, 78.900
Angle α, β, γ (deg.)90.00, 98.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9898, -0.12358, 0.07082), (-0.12169, 0.47539, -0.87132), (0.07402, -0.87105, -0.48558)
Vector: -4.85506, 17.46366, 30.28586)

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Components

#1: Protein PROTEIN (LACTOYLGLUTATHIONE LYASE) / GLYOXALASE I


Mass: 20672.520 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GIP / S-(N-HYDROXY-N-IODOPHENYLCARBAMOYL)GLUTATHIONE


Mass: 570.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23IN4O8S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE REFERENCE FOR THE SEQUENCE: 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: 2.9 Å3/Da / Density % sol: 49 %
Crystal growpH: 5.8
Details: PROTEIN WAS CRYSTALLISED BY EQILLABRATION AGAINST PEG 2000 MONOMETHLY ETHER, 50 MM MES PH 5.8, 0.1M NACL. HIPC-GSH WAS PRESENT IN THE PROTEIN SOLUTION
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: 263 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 3, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→29 Å / Num. obs: 28148 / % possible obs: 93.6 % / Redundancy: 1.8 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.83 / Net I/σ(I): 9
Reflection shellResolution: 2→2.11 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 3.2 / % possible all: 93.5
Reflection
*PLUS
Num. measured all: 49286
Reflection shell
*PLUS
% possible obs: 93.5 %

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Processing

Software
NameVersionClassification
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: OTHER / Resolution: 2→29 Å / SU B: 3.3 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1418 5 %RANDOM
Rwork0.178 ---
obs0.18 28134 94 %-
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 2→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 64 191 3055
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0230.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0230.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9532
X-RAY DIFFRACTIONp_mcangle_it1.5122.5
X-RAY DIFFRACTIONp_scbond_it3.1054
X-RAY DIFFRACTIONp_scangle_it4.6126
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.090.15
X-RAY DIFFRACTIONp_singtor_nbd0.1690.3
X-RAY DIFFRACTIONp_multtor_nbd0.230.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.57
X-RAY DIFFRACTIONp_staggered_tor15.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor36.420
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 29 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.090.15

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