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- PDB-1qh5: HUMAN GLYOXALASE II WITH S-(N-HYDROXY-N-BROMOPHENYLCARBAMOYL)GLUT... -

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Basic information

Entry
Database: PDB / ID: 1qh5
TitleHUMAN GLYOXALASE II WITH S-(N-HYDROXY-N-BROMOPHENYLCARBAMOYL)GLUTATHIONE
ComponentsPROTEIN (HYDROXYACYLGLUTATHIONE HYDROLASE)
KeywordsHYDROLASE / METALLO-HYDROLASE
Function / homology
Function and homology information


hydroxyacylglutathione hydrolase / hydroxyacylglutathione hydrolase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / glutathione biosynthetic process / Pyruvate metabolism / glutathione metabolic process / mitochondrial matrix / mitochondrion / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Hydroxyacylglutathione hydrolase / Hydroxyacylglutathione hydrolase, C-terminal domain / Hydroxyacylglutathione hydrolase, MBL domain / Hydroxyacylglutathione hydrolase C-terminus / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...Hydroxyacylglutathione hydrolase / Hydroxyacylglutathione hydrolase, C-terminal domain / Hydroxyacylglutathione hydrolase, MBL domain / Hydroxyacylglutathione hydrolase C-terminus / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
S-(N-HYDROXY-N-BROMOPHENYLCARBAMOYL)GLUTATHIONE / GLUTATHIONE / Hydroxyacylglutathione hydrolase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.45 Å
AuthorsCameron, A.D. / Ridderstrom, M. / Olin, B. / Mannervik, B.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of human glyoxalase II and its complex with a glutathione thiolester substrate analogue.
Authors: Cameron, A.D. / Ridderstrom, M. / Olin, B. / Mannervik, B.
History
DepositionMay 11, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Sep 24, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 14, 2011Group: Non-polymer description
Revision 1.4Dec 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_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_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_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: PROTEIN (HYDROXYACYLGLUTATHIONE HYDROLASE)
B: PROTEIN (HYDROXYACYLGLUTATHIONE HYDROLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9008
Polymers57,8082
Non-polymers1,0926
Water6,431357
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.550, 73.800, 164.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99987, -0.01367, 0.00851), (0.01567, -0.70323, 0.71079), (-0.00373, 0.71083, 0.70335)
Vector: 26.68236, 49.70305, -17.81793)

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Components

#1: Protein PROTEIN (HYDROXYACYLGLUTATHIONE HYDROLASE) / GLYOXALASE II


Mass: 28904.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: LIVER / Description: HETEROLOGOUSLY EXPRESSED / Plasmid: PKK 223-3,ACCI-DELETED / Production host: Escherichia coli (E. coli) / Strain (production host): JM 109
References: UniProt: Q16775, hydroxyacylglutathione hydrolase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-GBP / S-(N-HYDROXY-N-BROMOPHENYLCARBAMOYL)GLUTATHIONE


Mass: 523.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23BrN4O8S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 32 %
Crystal growpH: 6.5
Details: EQUILABRATION AGAINST 4-20% W/V PEG 2000 MONOMETHYL ETHER, pH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
210 mMMOPS1drop
325 %PEG4001drop
44-20 %mPEG20001reservoir
50.1 Msodium imidazole1reservoir
62 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9317
DetectorType: ADSC / Detector: CCD / Date: Nov 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9317 Å / Relative weight: 1
ReflectionResolution: 1.45→43 Å / Num. obs: 437671 / % possible obs: 99 % / Redundancy: 5.2 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 13
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4 / % possible all: 100
Reflection
*PLUS
Num. obs: 84815 / Num. measured all: 437671
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.34

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.45→20 Å / SU B: 1.3 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.08
RfactorNum. reflection% reflectionSelection details
Rfree0.232 4298 5 %RANDOM
Rwork0.204 ---
obs0.204 86596 99 %-
Displacement parametersBiso mean: 25.6 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 55 357 4468
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.272
X-RAY DIFFRACTIONp_mcangle_it1.8562.5
X-RAY DIFFRACTIONp_scbond_it2.9184
X-RAY DIFFRACTIONp_scangle_it4.1476
X-RAY DIFFRACTIONp_plane_restr0.0170.03
X-RAY DIFFRACTIONp_chiral_restr0.110.15
X-RAY DIFFRACTIONp_singtor_nbd0.1660.3
X-RAY DIFFRACTIONp_multtor_nbd0.240.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor47
X-RAY DIFFRACTIONp_staggered_tor1315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.03
X-RAY DIFFRACTIONp_chiral_restr0.150.11

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