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- PDB-2p1e: Crystal structure of the Leishmania infantum glyoxalase II with D... -

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Basic information

Entry
Database: PDB / ID: 2p1e
TitleCrystal structure of the Leishmania infantum glyoxalase II with D-Lactate at the active site
ComponentsGlyoxalase II
KeywordsHYDROLASE / Beta sandwich / product / spermidine
Function / homology
Function and homology information


hydroxyacylglutathione hydrolase / hydroxyacylglutathione hydrolase activity / metal ion binding
Similarity search - Function
Hydroxyacylglutathione hydrolase, C-terminal domain / Hydroxyacylglutathione hydrolase, MBL domain / Hydroxyacylglutathione hydrolase C-terminus / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
LACTIC ACID / SPERMIDINE / Putative glyoxalase II
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTrincao, J. / Barata, L. / Najmudin, S. / Bonifacio, C. / Romao, M.J.
CitationJournal: Biochemistry / Year: 2008
Title: Catalysis and Structural Properties of Leishmania infantum Glyoxalase II: Trypanothione Specificity and Phylogeny.
Authors: Silva, M.S. / Barata, L. / Ferreira, A.E. / Romao, S. / Tomas, A.M. / Freire, A.P. / Cordeiro, C.
History
DepositionMar 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyoxalase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7895
Polymers34,4231
Non-polymers3664
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.172, 89.121, 85.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Glyoxalase II


Mass: 34422.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: GLOII / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus
References: UniProt: Q2PYN0, hydroxyacylglutathione hydrolase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#4: Chemical ChemComp-LAC / LACTIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.87 Å3/Da / Density % sol: 34.17 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% PEG 8K, 0.2M MgCl2, 0.1M ammonium acetate - soaked 30 min in 40% PEG 8K, 0.2M MgCl2, 0.1M ammonium acetate, 10mM S-D-lactoyltrypanothione, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9538
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2006 / Details: Undulator
RadiationMonochromator: Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9538 Å / Relative weight: 1
ReflectionResolution: 1.9→53.642 Å / Num. all: 20715 / Num. obs: 20715 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 5.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 1.5 / Num. measured all: 41988 / Num. unique all: 2983 / Rsym value: 0.488 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.7 Å25.89 Å
Translation2.7 Å25.89 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MxCuBEdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2P18

2p18


Resolution: 1.9→53.61 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.955 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.162 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1060 5.1 %RANDOM
Rwork0.181 ---
all0.261 20692 --
obs0.183 20692 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.204 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.06 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→53.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2129 0 18 102 2249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222215
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9383013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7245280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25124.14199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51715328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.365158
X-RAY DIFFRACTIONr_chiral_restr0.1160.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021708
X-RAY DIFFRACTIONr_nbd_refined0.2080.21065
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2115
X-RAY DIFFRACTIONr_metal_ion_refined0.0240.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.27
X-RAY DIFFRACTIONr_mcbond_it0.8311.51426
X-RAY DIFFRACTIONr_mcangle_it1.2222244
X-RAY DIFFRACTIONr_scbond_it2.2423882
X-RAY DIFFRACTIONr_scangle_it3.1394.5768
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 60 -
Rwork0.191 1435 -
obs-1495 99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.67910.79090.96122.8438-0.50741.5683-0.1024-0.84260.44090.5184-0.0549-0.1696-0.1258-0.03420.1573-0.0167-0.0161-0.00910.1077-0.1253-0.082521.13233.60961.866
211.99574.52521.329712.42437.66636.6020.2832-1.46640.68410.2079-0.05190.0913-0.3257-0.1282-0.23130.1140.01370.10380.3582-0.1608-0.060514.39636.01568.74
36.2031-1.23350.52275.22381.96986.2221-0.2368-0.78550.74970.3590.13580.2446-0.1445-0.33140.101-0.12090.04560.0313-0.0126-0.1008-0.00779.44335.16855.209
44.4959-2.84993.96322.2338-1.56475.5944-0.3414-0.99760.73860.84880.4802-0.9873-1.0829-0.7658-0.13880.33020.01930.07560.2401-0.36450.56329.88346.1358.712
52.8886-0.61870.17643.1649-0.3311.54570.099-0.13180.49620.0123-0.0778-0.1396-0.10430.0469-0.0212-0.127-0.01160.0408-0.1226-0.0234-0.078519.14133.547.133
614.18935.8644.03067.2383.03465.49310.06180.5632-0.2019-0.5032-0.06560.0270.1946-0.01660.0038-0.04530.0669-0.0128-0.10120.0032-0.17920.51921.96337.962
73.68150.5242-0.24072.95070.05430.74450.0827-0.1552-0.1905-0.0491-0.0332-0.21560.15830.1109-0.0494-0.10390.0103-0.0298-0.08690.0258-0.159328.720.6549.381
810.3691-4.7135-9.7526.85295.875715.8487-0.0726-0.6183-0.69210.3934-0.05270.01980.40360.45740.12540.00010.0208-0.0980.05560.1181-0.079432.08511.48257.134
94.3882-0.47530.18141.97361.24514.42970.14730.0774-0.35860.02430.0153-0.05530.17010.2545-0.1626-0.1090.0159-0.0302-0.12370.0213-0.124928.63616.38546.156
1018.63171.6097-0.1416.43580.741211.93260.16810.4987-1.22920.5065-0.27190.72280.4537-0.51380.10380.0178-0.0054-0.0595-0.0804-0.06120.038819.17110.04240.475
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 4517 - 61
2246 - 5662 - 72
3369 - 9085 - 106
4491 - 103107 - 119
55104 - 177120 - 193
66178 - 189194 - 205
77190 - 226206 - 242
88227 - 247243 - 263
99248 - 284264 - 300
1010285 - 293301 - 309

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