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- PDB-1f9z: CRYSTAL STRUCTURE OF THE NI(II)-BOUND GLYOXALASE I FROM ESCHERICH... -

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Basic information

Entry
Database: PDB / ID: 1f9z
TitleCRYSTAL STRUCTURE OF THE NI(II)-BOUND GLYOXALASE I FROM ESCHERICHIA COLI
ComponentsGLYOXALASE I
KeywordsLYASE / Beta-Alpha-Beta-Beta-Beta motif / Protein-Ni(II) complex / homodimer
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
NICKEL (II) ION / Lactoylglutathione lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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 11, 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, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 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_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)29,9914
Polymers29,8742
Non-polymers1172
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-41 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.047, 56.478, 46.705
Angle α, β, γ (deg.)90.00, 95.44, 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 2-fold non-crystallographic symmetry.

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Components

#1: Protein GLYOXALASE I / 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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 39.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG1000, PEG8000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
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: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.78
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.78 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 38619 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.8
Reflection shellResolution: 1.49→1.57 Å / Redundancy: 3 % / Rmerge(I) obs: 0.29 / % possible all: 98
Reflection
*PLUS
Num. measured all: 116872
Reflection shell
*PLUS
% possible obs: 98 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
SHARPphasing
TNTrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.5→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
Rfree0.272 1909 5 %Thin Shells
Rwork0.205 ---
all0.211 38192 --
obs0.211 38192 98.9 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 150 Å2 / ksol: 0.79 e/Å3
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 2 262 2266
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0120380.8
X-RAY DIFFRACTIONt_angle_deg1.98727441.3
X-RAY DIFFRACTIONt_dihedral_angle_d16.71712140
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle00
X-RAY DIFFRACTIONt_trig_c_planes0.007602
X-RAY DIFFRACTIONt_gen_planes0.0122925
X-RAY DIFFRACTIONt_it3.44620381
X-RAY DIFFRACTIONt_nbd0.0193310
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.205 / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.987

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