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- PDB-1fa7: CRYSTAL STRUCTURE OF CD(II)-BOUND GLYOXALASE I OF ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1fa7
TitleCRYSTAL STRUCTURE OF CD(II)-BOUND GLYOXALASE I OF ESCHERICHIA COLI
ComponentsGLYOXALASE ILactoylglutathione lyase
KeywordsLYASE / Beta-Alpha-Beta-Beta-Beta motif / homodimer / protein-Cd(II) complex
Function / homology
Function and homology information


lactoylglutathione lyase / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / lactoylglutathione lyase activity / nickel cation binding / response to toxic substance / protein homodimerization activity / 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
: / Lactoylglutathione lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsHe, M.M. / Clugston, S.L. / Honek, J.F. / Matthews, B.W.
CitationJournal: Biochemistry / Year: 2000
Title: Determination of the structure of Escherichia coli glyoxalase I suggests a structural basis for differential metal activation.
Authors: He, M.M. / Clugston, S.L. / Honek, J.F. / Matthews, B.W.
History
DepositionJul 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: 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_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)30,0984
Polymers29,8742
Non-polymers2252
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-35 kcal/mol
Surface area12560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.930, 56.390, 46.790
Angle α, β, γ (deg.)90.00, 95.24, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a homodimer in each asymmetric unit and the two monomers are related by non-crystallographic symmetry

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Components

#1: Protein GLYOXALASE I / Lactoylglutathione lyase / LACTOYLGLUTATHIONE LYASE


Mass: 14936.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC81, lactoylglutathione lyase
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 298 K / pH: 5
Details: PEG 1000, PEG 8000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112-37 mg/mlprotein1drop
25-10 %PEG10001reservoir
35-10 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 19871 / % possible obs: 90.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.27 / % possible all: 90
Reflection
*PLUS
Num. measured all: 47320 / Rmerge(I) obs: 0.102
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
AMoREphasing
TNTrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.9→20 Å / Isotropic thermal model: TNT BCORREL VERSION 1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO VERSION 1.0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 826 5 %Thin Shells
Rwork0.177 ---
all0.183 17009 --
obs0.183 17009 90.3 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 150 Å2 / ksol: 0.72 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 2 259 2263
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00720360.8
X-RAY DIFFRACTIONt_angle_deg1.56227421.3
X-RAY DIFFRACTIONt_dihedral_angle_d16.77912140
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle00
X-RAY DIFFRACTIONt_trig_c_planes0.004582
X-RAY DIFFRACTIONt_gen_planes0.0082925
X-RAY DIFFRACTIONt_it3.90720361
X-RAY DIFFRACTIONt_nbd0.0224410
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor all: 0.18 / Rfactor obs: 0.177 / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.007
X-RAY DIFFRACTIONt_angle_deg1.58

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