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- PDB-6s0i: Crystal structure of Escherichia coli Glyoxalase II with L-Tartra... -

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Basic information

Entry
Database: PDB / ID: 6s0i
TitleCrystal structure of Escherichia coli Glyoxalase II with L-Tartrate in the active site
ComponentsHydroxyacylglutathione hydrolase GloB
KeywordsHYDROLASE / Metallo-beta-lactamase / metal-ion-binding / Glyoxalase II (hydroxyacylglutathione hydrolase) / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Function / homology
Function and homology information


hydroxyacylglutathione hydrolase / hydroxyacylglutathione hydrolase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / response to toxic substance / response to heat / zinc ion binding
Similarity search - Function
Hydroxyacylglutathione hydrolase / Hydroxyacylglutathione hydrolase, C-terminal domain / Hydroxyacylglutathione hydrolase, MBL domain / Hydroxyacylglutathione hydrolase C-terminus / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...Hydroxyacylglutathione hydrolase / Hydroxyacylglutathione hydrolase, C-terminal domain / Hydroxyacylglutathione hydrolase, MBL domain / Hydroxyacylglutathione hydrolase C-terminus / Metallo-beta-lactamase superfamily / 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
L(+)-TARTARIC ACID / Hydroxyacylglutathione hydrolase GloB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.803 Å
AuthorsSkorupskaite, A. / McDonough, M.A. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M011224/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of Escherichia coli Glyoxalase II
Authors: Skorupskaite, A. / McDonough, M.A. / Brem, J. / Schofield, C.J.
History
DepositionJun 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxyacylglutathione hydrolase GloB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9875
Polymers28,4671
Non-polymers5194
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Non-denaturing MS, gel filtration, monomer observed
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-75 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.053, 43.655, 159.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hydroxyacylglutathione hydrolase GloB / Glyoxalase II / Glx II


Mass: 28467.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: gloB, yafR, b0212, JW0202 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AC84, 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-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.35 % / Description: Rhombohedral rod
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02M Sodium formate, 0.02M Ammonium acetate, 0.02M Sodium citrate tribasic dihydrate, 0.02M Sodium potassium tartrate tetrahydrate, 0.02M Sodium oxamate; 0.1 M sodium HEPES and MOPS (acid), ...Details: 0.02M Sodium formate, 0.02M Ammonium acetate, 0.02M Sodium citrate tribasic dihydrate, 0.02M Sodium potassium tartrate tetrahydrate, 0.02M Sodium oxamate; 0.1 M sodium HEPES and MOPS (acid), pH 7.5; 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.8→29.4 Å / Num. obs: 25769 / % possible obs: 99 % / Redundancy: 11.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.031 / Rrim(I) all: 0.107 / Net I/σ(I): 16.4 / Num. measured all: 298754 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.856.70.6931115116700.7860.2770.752.389.7
8.06-29.49.60.04534063530.9990.0150.04842.797.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Aimless0.7.3data scaling
PHASER1.13phasing
PDB_EXTRACT3.25data extraction
XDSVERSION Jan 26, 2018 BUILT=20180808data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RZ0

6rz0


Resolution: 1.803→29.398 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.86
RfactorNum. reflection% reflection
Rfree0.1969 2000 7.78 %
Rwork0.1614 --
obs0.164 25700 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.5 Å2 / Biso mean: 29.8172 Å2 / Biso min: 12.43 Å2
Refinement stepCycle: final / Resolution: 1.803→29.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 34 230 2195
Biso mean--44.62 37.84 -
Num. residues----251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8033-1.84840.2891250.2491492161789
1.8484-1.89840.27121380.22381623176197
1.8984-1.95420.22341430.184817001843100
1.9542-2.01730.20781410.168716621803100
2.0173-2.08940.16741420.168716821824100
2.0894-2.1730.20661430.15917021845100
2.173-2.27180.17091410.149316761817100
2.2718-2.39160.1681420.143916861828100
2.3916-2.54130.20551440.141317001844100
2.5413-2.73740.19571450.15817141859100
2.7374-3.01270.1781450.16817081853100
3.0127-3.4480.18441460.162717361882100
3.448-4.34190.17681490.139417661915100
4.3419-29.40190.22611560.169718532009100
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)
13.14210.1884-1.11591.9627-1.11544.85510.0253-0.29630.06370.16540.04910.1023-0.143-0.1776-0.06790.15290.00990.00240.1584-0.02830.1208-0.22350.9514-8.4192
22.56140.4259-0.31841.95380.31354.63150.0041-0.2948-0.05640.2435-0.02-0.10850.15120.2320.00750.14770.0207-0.02420.1860.01040.129910.3371-6.52-11.0465
36.60365.80833.52646.70064.20472.7631-0.0998-0.1920.4214-0.1225-0.09280.21790.01730.04880.17940.1320.0157-0.00520.17580.02520.135110.60411.3967-26.4794
42.0872-0.25660.16161.4526-0.55012.23460.02810.0686-0.0013-0.10280.0211-0.00180.15590.0659-0.05880.1234-0.0183-0.00010.1284-0.00840.13195.2043-4.6742-30.4598
58.6442-7.7313-7.34157.73366.73566.25780.02270.3292-0.1252-0.1482-0.1710.21120.0833-0.30590.21930.1558-0.0235-0.02650.18680.0190.1879-9.1298-0.818-34.5075
67.5156-0.7762-3.26980.69440.16284.8778-0.03040.1031-0.0938-0.05520.0859-0.06010.27510.0539-0.01370.1561-0.0193-0.04040.136-0.01140.143-0.2853-6.5846-30.6825
76.7448-3.80826.11395.539-4.57199.57670.20570.70550.5773-0.3093-0.1121-0.7312-0.37530.6921-0.06620.3639-0.00340.10580.364-0.05740.33713.4432-5.2504-46.1837
84.4779-5.96623.218.5914-3.22396.14180.24180.4434-0.0547-0.4329-0.1726-0.03590.22690.2688-0.02140.1737-0.04250.00170.2191-0.00160.222913.49570.5822-37.3277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 68 )A1 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 126 )A69 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 141 )A127 - 141
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 182 )A142 - 182
5X-RAY DIFFRACTION5chain 'A' and (resid 183 through 198 )A183 - 198
6X-RAY DIFFRACTION6chain 'A' and (resid 199 through 221 )A199 - 221
7X-RAY DIFFRACTION7chain 'A' and (resid 222 through 236 )A222 - 236
8X-RAY DIFFRACTION8chain 'A' and (resid 237 through 251 )A237 - 251

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