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- PDB-2za0: Crystal structure of mouse glyoxalase I complexed with methyl-gerfelin -

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Basic information

Entry
Database: PDB / ID: 2za0
TitleCrystal structure of mouse glyoxalase I complexed with methyl-gerfelin
ComponentsGlyoxalase I
KeywordsLYASE / LACTOYLGLUTATHIONE LYASE / GLYOXALASE I / METHYL-GERFELIN
Function / homology
Function and homology information


Pyruvate metabolism / lactoylglutathione lyase / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / lactoylglutathione lyase activity / methylglyoxal metabolic process / glutathione metabolic process / osteoclast differentiation / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / zinc ion binding ...Pyruvate metabolism / lactoylglutathione lyase / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / lactoylglutathione lyase activity / methylglyoxal metabolic process / glutathione metabolic process / osteoclast differentiation / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / plasma membrane / 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
Chem-MGI / Lactoylglutathione lyase / Lactoylglutathione lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOkumura, H. / Kawatani, M. / Osada, H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: The identification of an osteoclastogenesis inhibitor through the inhibition of glyoxalase I
Authors: Kawatani, M. / Okumura, H. / Honda, K. / Kanoh, N. / Muroi, M. / Dohmae, N. / Takami, M. / Kitagawa, M. / Futamura, Y. / Imoto, M. / Osada, H.
History
DepositionSep 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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: Glyoxalase I
B: Glyoxalase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4116
Polymers41,6712
Non-polymers7394
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-142.9 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.982, 65.314, 66.159
Angle α, β, γ (deg.)90.00, 101.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glyoxalase I


Mass: 20835.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Glo1 / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: A5GZX3, UniProt: Q9CPU0*PLUS, 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-MGI / methyl 4-(2,3-dihydroxy-5-methylphenoxy)-2-hydroxy-6-methylbenzoate / methyl-gerfelin


Mass: 304.295 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.8
Details: PEG2000mme, MES, NaCl, pH5.8, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.7 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 5, 2007
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 38740 / Num. obs: 36563 / % possible obs: 94.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 17.53
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 3.15 / Rsym value: 0.301 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QIP

1qip


Resolution: 1.7→23.38 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 984855.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1841 5 %RANDOM
Rwork0.185 ---
obs-36510 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.5238 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.99 Å2
2--0.27 Å20 Å2
3----0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→23.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 46 392 3283
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.72
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 306 4.8 %
Rwork0.211 6118 -
obs-3872 100 %

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