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- PDB-4mtq: Ni-bound GloA2 -

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Basic information

Entry
Database: PDB / ID: 4mtq
TitleNi-bound GloA2
ComponentsLactoylglutathione lyase
KeywordsLYASE / isomerase / hydrolase / metal binding
Function / homology
Function and homology information


methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / lactoylglutathione lyase activity / metal ion binding / cytoplasm
Similarity search - Function
Glyoxalase I / 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 / SUCCINIC ACID / Aldoketomutase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsBythell-Douglas, R. / Bond, C.S.
CitationJournal: Chemistry / Year: 2015
Title: The crystal structure of a homodimeric Pseudomonas glyoxalase I enzyme reveals asymmetric metallation commensurate with half-of-sites activity.
Authors: Bythell-Douglas, R. / Suttisansanee, U. / Flematti, G.R. / Challenor, M. / Lee, M. / Panjikar, S. / Honek, J.F. / Bond, C.S.
History
DepositionSep 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Sep 20, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Lactoylglutathione lyase
B: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1886
Polymers29,8942
Non-polymers2944
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-49 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.145, 74.983, 80.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lactoylglutathione lyase / / GloA2


Mass: 14946.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: gloA2, PA0710 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q9I5L8, lactoylglutathione lyase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.3
Details: 0.1 M succinic acid, 21% PEG3350, pH 6.3, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.17→19.84 Å / Num. obs: 13652 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 40.91 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.032 / Net I/σ(I): 16.1
Reflection shellResolution: 2.17→2.28 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1810 / Rsym value: 0.688 / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MTR

4mtr


Resolution: 2.17→19.41 Å / Cor.coef. Fo:Fc: 0.9573 / Cor.coef. Fo:Fc free: 0.9367 / SU R Cruickshank DPI: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.255 / SU Rfree Blow DPI: 0.197 / SU Rfree Cruickshank DPI: 0.196 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 660 4.86 %RANDOM
Rwork0.1828 ---
all0.1853 13652 --
obs0.1853 13572 99.21 %-
Displacement parametersBiso mean: 48.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.3354 Å20 Å20 Å2
2---0.0597 Å20 Å2
3---0.3951 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å
Refinement stepCycle: LAST / Resolution: 2.17→19.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 11 70 2043
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d718SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes305HARMONIC5
X-RAY DIFFRACTIONt_it2010HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion246SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2186SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2010HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2709HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion16.31
LS refinement shellResolution: 2.17→2.34 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2878 136 5.14 %
Rwork0.2474 2511 -
all0.2496 2647 -
obs--99.21 %

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