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- PDB-2c21: Specificity of the Trypanothione-dependednt Leishmania major Glyo... -

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Basic information

Entry
Database: PDB / ID: 2c21
TitleSpecificity of the Trypanothione-dependednt Leishmania major Glyoxalase I: Structure and biochemical comparison with the human enzyme
ComponentsTRYPANOTHIONE-DEPENDENT GLYOXALASE I
KeywordsLYASE / GLYOXALASE I / LEISHMANIA MAJOR / TRYPANOTHIONE / GLUTATHIONYLSPERMIDINE / METHYLGLYOXAL / DETOXIFICATION
Function / homology
Function and homology information


lactoylglutathione lyase / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / lactoylglutathione lyase activity / metal ion binding / cytoplasm
Similarity search - Function
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 ...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 / Glyoxalase I
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAriza, A. / Vickers, T.J. / Greig, N. / Armour, K.A. / Eggleston, I.M. / Fairlamb, A.H. / Bond, C.S.
CitationJournal: Mol.Microbiol. / Year: 2006
Title: Specificity of the Trypanothione-Dependent Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme.
Authors: Ariza, A. / Vickers, T.J. / Greig, N. / Armour, K.A. / Dixon, M.J. / Eggleston, I.M. / Fairlamb, A.H. / Bond, C.S.
History
DepositionSep 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPANOTHIONE-DEPENDENT GLYOXALASE I
B: TRYPANOTHIONE-DEPENDENT GLYOXALASE I
C: TRYPANOTHIONE-DEPENDENT GLYOXALASE I
D: TRYPANOTHIONE-DEPENDENT GLYOXALASE I
E: TRYPANOTHIONE-DEPENDENT GLYOXALASE I
F: TRYPANOTHIONE-DEPENDENT GLYOXALASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,07522
Polymers99,7316
Non-polymers1,34416
Water15,115839
1
A: TRYPANOTHIONE-DEPENDENT GLYOXALASE I
B: TRYPANOTHIONE-DEPENDENT GLYOXALASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7398
Polymers33,2442
Non-polymers4956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: TRYPANOTHIONE-DEPENDENT GLYOXALASE I
D: TRYPANOTHIONE-DEPENDENT GLYOXALASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8579
Polymers33,2442
Non-polymers6137
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: TRYPANOTHIONE-DEPENDENT GLYOXALASE I
F: TRYPANOTHIONE-DEPENDENT GLYOXALASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4795
Polymers33,2442
Non-polymers2363
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)130.193, 148.957, 50.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 3 - 141 / Label seq-ID: 6 - 144

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

NCS oper:
IDCodeMatrixVector
1given(-0.934961, -0.348219, 0.06775), (-0.352939, 0.893807, -0.276662), (0.035783, -0.28258, -0.958575)67.4877, 17.9133, 36.1849
2given(-0.41519, 0.907263, -0.067004), (-0.879978, -0.381836, 0.282557), (0.230769, 0.176277, 0.956907)35.5656, 44.801, -1.9631
3given(0.708185, -0.706005, 0.00547), (-0.706018, -0.708119, 0.010187), (-0.003318, -0.011077, -0.999933)18.7717, 45.9082, 27.0539
4given(-0.656057, -0.704095, 0.27173), (0.75458, -0.618644, 0.218831), (0.014026, 0.348608, 0.937163)60.6862, -3.541, 9.8367
5given(0.339436, 0.897001, -0.283146), (0.900126, -0.397134, -0.179041), (-0.273047, -0.194094, -0.942216)12.5815, -9.4216, 30.368

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
TRYPANOTHIONE-DEPENDENT GLYOXALASE I


Mass: 16621.896 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: FRIEDLIN A1 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q68RJ8, Lyases; Carbon-carbon lyases; Carboxy-lyases

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Non-polymers , 5 types, 855 molecules

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


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 839 / 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: 2.24 Å3/Da / Density % sol: 44.64 %
Crystal growpH: 8 / Details: 62% (V/V) MPD, 100MM TRIS-HCL PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 16, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→60 Å / Num. obs: 67613 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 28.36 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.9 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FA8

1fa8


Resolution: 2→129.1 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.709 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3378 5 %RANDOM
Rwork0.155 ---
obs0.157 64010 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.3 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 2→129.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6768 0 72 839 7679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227136
X-RAY DIFFRACTIONr_bond_other_d0.0010.026586
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9849627
X-RAY DIFFRACTIONr_angle_other_deg0.758315352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9925848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43923.9341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28151373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8451547
X-RAY DIFFRACTIONr_chiral_restr0.0760.21042
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027721
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021440
X-RAY DIFFRACTIONr_nbd_refined0.1940.21206
X-RAY DIFFRACTIONr_nbd_other0.1760.26353
X-RAY DIFFRACTIONr_nbtor_refined0.1770.23319
X-RAY DIFFRACTIONr_nbtor_other0.080.24199
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4911.54189
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87526821
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.52933034
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3514.52796
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2149 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.485
2Bloose positional0.395
3Cloose positional0.345
4Dloose positional0.455
5Eloose positional0.45
6Floose positional0.495
1Aloose thermal1.3410
2Bloose thermal1.3810
3Cloose thermal1.3410
4Dloose thermal1.1810
5Eloose thermal1.1710
6Floose thermal1.6210
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.232 249
Rwork0.192 4617
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)
12.0295-0.0584-0.04122.1524-0.47143.4238-0.0052-0.1493-0.0440.1533-0.00870.22610.5034-0.69460.0139-0.0947-0.18990.0026-0.01920.0256-0.200430.7937-7.676930.2588
24.0836-0.6012-0.77083.24750.46993.3150.06680.4713-0.1968-0.5507-0.10010.73770.3919-1.11990.0333-0.0322-0.23-0.12030.19880.0361-0.07624.1559-8.365113.532
317.16173.6437-8.59495.33591.107511.1979-0.46040.4465-1.2447-0.662-0.0235-0.13831.1545-0.52480.48390.493-0.15970.0288-0.1962-0.0925-0.037240.0007-21.33755.2019
41.2327-0.28040.00532.6217-1.27192.7529-0.00180.1611-0.2922-0.4353-0.0084-0.03220.8122-0.11110.01020.0397-0.07040.0057-0.2339-0.0235-0.212943.1766-8.491410.3183
52.82490.20840.5712.9115-1.5973.89680.0379-0.4679-0.13010.2654-0.118-0.19710.19010.11410.08-0.1578-0.0378-0.0068-0.19560.0215-0.238148.947-2.032726.0852
617.17832.6859-7.42432.0871-1.69526.1227-0.0207-0.6778-0.58960.3772-0.274-0.13070.7193-0.07640.29460.1937-0.2122-0.0145-0.040.1579-0.135238.3776-16.726838.4825
72.0260.9213-0.78111.5155-1.05872.50310.1844-0.31970.20730.33-0.1501-0.1367-0.33450.3829-0.0343-0.1599-0.08430.017-0.1908-0.0373-0.211955.658121.404916.2789
83.2188-0.0217-1.56582.9729-0.67922.97170.04970.2515-0.0584-0.3932-0.0702-0.17520.23270.14830.0206-0.19680.02270.0327-0.245-0.0118-0.24955.129812.71970.5197
98.9136-10.04926.266213.6629-8.60046.40760.10790.62270.694-0.5276-0.3516-0.6558-0.12360.52060.2437-0.0244-0.04190.1478-0.07460.0948-0.130157.980330.5851-11.9829
102.52450.3974-0.21471.6144-0.24822.4290.04180.24820.2728-0.1178-0.01380.0944-0.34930.0309-0.028-0.13840.00760.0729-0.2810.0202-0.184446.322529.433-3.6902
114.19620.22731.23932.5650.67461.60150.0296-0.50520.52110.4161-0.06880.1781-0.4034-0.1810.0392-0.0260.00940.1228-0.2167-0.0712-0.090842.224834.780213.0364
129.0268-8.60487.316314.6615-7.55286.59240.1528-0.48090.45890.7317-0.4266-0.3685-0.65780.30930.27380.0196-0.2166-0.0191-0.0331-0.1041-0.073962.647932.833821.2273
135.9141-1.13540.26531.86110.81292.40610.0986-0.54450.35570.2489-0.1680.4275-0.2707-0.63370.0693-0.10950.09550.1602-0.0211-0.0610.071516.717230.759710.0904
144.32650.01590.06581.79640.05154.06050.21960.84430.3598-0.4677-0.25280.2046-0.4011-0.63480.0331-0.07970.21110.05480.05310.02930.038120.392730.0157-7.6324
158.9395.0795-0.680814.27421.55634.37380.33431.6077-0.3527-0.3534-0.46660.9346-0.154-1.45330.1324-0.0710.2548-0.10610.9952-0.14350.39110.020723.8605-13.7129
165.1234-1.09540.24554.43520.83683.22720.11840.9543-0.5661-0.2949-0.36280.54430.1742-1.0030.2444-0.20370.01590.04930.3982-0.2160.29787.782815.6583-5.3856
175.88040.3056-0.47854.18420.26363.0083-0.101-0.6682-1.01570.9452-0.14390.46080.6014-0.60850.24490.0436-0.1390.20580.14570.03130.34979.456213.262212.4895
1811.971112.72092.007525.73475.47951.25320.4304-0.56470.09851.0134-0.63250.7745-0.1495-1.08690.20220.04320.1240.28910.284-0.22160.21375.327734.187617.9647
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 67
2X-RAY DIFFRACTION2A68 - 123
3X-RAY DIFFRACTION3A124 - 141
4X-RAY DIFFRACTION4B3 - 67
5X-RAY DIFFRACTION5B68 - 123
6X-RAY DIFFRACTION6B124 - 141
7X-RAY DIFFRACTION7C3 - 67
8X-RAY DIFFRACTION8C68 - 123
9X-RAY DIFFRACTION9C124 - 141
10X-RAY DIFFRACTION10D3 - 67
11X-RAY DIFFRACTION11D68 - 123
12X-RAY DIFFRACTION12D124 - 141
13X-RAY DIFFRACTION13E3 - 67
14X-RAY DIFFRACTION14E68 - 123
15X-RAY DIFFRACTION15E124 - 141
16X-RAY DIFFRACTION16F3 - 67
17X-RAY DIFFRACTION17F68 - 123
18X-RAY DIFFRACTION18F124 - 141

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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