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- PDB-5d7z: Crystal structure of glyoxalase I from Zea mays -

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Basic information

Entry
Database: PDB / ID: 5d7z
TitleCrystal structure of glyoxalase I from Zea mays
ComponentsLactoylglutathione lyase
KeywordsLYASE
Function / homology
Function and homology information


lactoylglutathione lyase / lactoylglutathione lyase activity / metal ion binding
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
FORMIC ACID / NICKEL (II) ION / Lactoylglutathione lyase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsGonzalez, J.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of the novel monomeric glyoxalase I from Zea mays.
Authors: Turra, G.L. / Agostini, R.B. / Fauguel, C.M. / Presello, D.A. / Andreo, C.S. / Gonzalez, J.M. / Campos-Bermudez, V.A.
History
DepositionAug 14, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionSep 9, 2015ID: 4RO6
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Mar 6, 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 / pdbx_struct_oper_list / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1859
Polymers33,4591
Non-polymers7268
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.690, 90.690, 74.713
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-301-

NI

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lactoylglutathione lyase / Glyoxalase I


Mass: 33458.922 Da / Num. of mol.: 1 / Fragment: UNP residues 26-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: Zm.67052, ZEAMMB73_635823 / Production host: Escherichia coli (E. coli) / References: UniProt: B6TPH0, lactoylglutathione lyase

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Non-polymers , 5 types, 154 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.7 / Details: 4M SODIUM FORMATE, 1% PEG 4000, PH 9.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.73→38.8 Å / Num. obs: 36195 / % possible obs: 99.7 % / Redundancy: 4.7 % / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→38.8 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.316 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20213 1843 5.1 %RANDOM
Rwork0.16614 ---
obs0.16802 34334 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.734 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.39 Å2-0 Å2
2--0.79 Å20 Å2
3----2.55 Å2
Refinement stepCycle: 1 / Resolution: 1.73→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 42 146 2389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192308
X-RAY DIFFRACTIONr_bond_other_d0.0020.022155
X-RAY DIFFRACTIONr_angle_refined_deg2.0261.9723103
X-RAY DIFFRACTIONr_angle_other_deg0.95334963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9395284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43724.19105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34815372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7351511
X-RAY DIFFRACTIONr_chiral_restr0.1250.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02524
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0472.8661128
X-RAY DIFFRACTIONr_mcbond_other3.0462.8671129
X-RAY DIFFRACTIONr_mcangle_it3.984.2751410
X-RAY DIFFRACTIONr_mcangle_other3.9794.2751410
X-RAY DIFFRACTIONr_scbond_it3.9945.2671178
X-RAY DIFFRACTIONr_scbond_other3.9935.2671178
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6824.6461692
X-RAY DIFFRACTIONr_long_range_B_refined7.16723.5692556
X-RAY DIFFRACTIONr_long_range_B_other7.1323.3632515
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded27.62651
LS refinement shellResolution: 1.734→1.779 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 153 -
Rwork0.288 2455 -
obs--96.27 %

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