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- PDB-6rz0: Crystal structure of Escherichia coli Glyoxalase II -

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Basic information

Entry
Database: PDB / ID: 6rz0
TitleCrystal structure of Escherichia coli Glyoxalase II
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
Hydroxyacylglutathione hydrolase GloB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 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 12, 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 / pdbx_struct_conn_angle / 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_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_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_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

Downloads & links

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Assembly

Deposited unit
A: Hydroxyacylglutathione hydrolase GloB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1139
Polymers28,4671
Non-polymers6468
Water8,215456
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 area970 Å2
ΔGint-120 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.382, 63.383, 72.726
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 464 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5 / Details: 0.1 M CAPS/NaOH pH 10.5, 0.2 M NaCl, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 0.99→47.79 Å / Num. obs: 135359 / % possible obs: 87.4 % / Redundancy: 10.7 % / Biso Wilson estimate: 7.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.018 / Rrim(I) all: 0.062 / Net I/σ(I): 24.9 / Num. measured all: 1447737 / Scaling rejects: 228
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
0.99-1.043.10.3822420277920.8130.2440.4583.535
3.12-47.7911.70.0556120252470.9970.0160.05841.899.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QED

2qed


Resolution: 1.1→47.783 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 10.39
RfactorNum. reflection% reflection
Rfree0.1281 3176 1.48 %
Rwork0.1192 --
obs0.1193 214302 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.21 Å2 / Biso mean: 11.8566 Å2 / Biso min: 1.01 Å2
Refinement stepCycle: final / Resolution: 1.1→47.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 0 45 496 2526
Biso mean--22.73 23.6 -
Num. residues----251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.11640.12911040.13758576868093
1.1164-1.13390.12391460.13428987913397
1.1339-1.15250.12441400.128592459385100
1.1525-1.17230.13291370.128191669303100
1.1723-1.19370.13551250.12592769401100
1.1937-1.21660.13831440.12891909334100
1.2166-1.24150.11031280.123992729400100
1.2415-1.26850.12591620.121191839345100
1.2685-1.2980.11551250.120692129337100
1.298-1.33040.12841290.123391999328100
1.3304-1.36640.12171680.122392509418100
1.3664-1.40660.12841240.117892049328100
1.4066-1.4520.1321450.115792309375100
1.452-1.50390.11621400.111892229362100
1.5039-1.56410.13821410.112192379378100
1.5641-1.63530.13891460.111991759321100
1.6353-1.72150.12141310.115892729403100
1.7215-1.82940.15041400.116991959335100
1.8294-1.97070.14541330.117592399372100
1.9707-2.1690.11931420.113491879329100
2.169-2.48280.11451450.108892319376100
2.4828-3.1280.12211410.117791789319100
3.128-47.82770.13431400.12792009340100
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)
10.7334-0.1077-0.11870.39340.10090.492-0.0047-0.0011-0.00070.0001-0.00750.03720.0057-0.0450.0120.0423-0.00150.00180.0389-0.00290.04441.702740.821332.6222
21.76632.78570.32124.5050.43940.3418-0.03640.0559-0.0365-0.10920.0595-0.0586-0.00880.0375-0.02610.04420.00880.00320.04980.00010.043357.091734.504225.9685
31.2510.6925-0.1421.0769-0.1381.02460.0545-0.1033-0.0960.0987-0.0458-0.06760.05940.0434-0.00330.05770.01610.00540.0282-0.00460.052155.347129.294733.0961
43.3872-2.9957-1.17273.38340.83780.49610.01170.07250.0116-0.0026-0.0179-0.03410.00760.013-0.00450.05020.00120.00520.046-0.01530.038158.472319.553518.3183
55.0988-2.79391.79612.8562-1.05082.70560.05710.0223-0.2523-0.03840.00710.07140.11160.0076-0.05880.0469-0.00470.0040.0324-0.00840.048949.137616.06318.4979
61.78860.14880.04361.13840.06832.21420.0017-0.1121-0.12070.10560.0022-0.09540.11690.1674-0.01140.08230.01440.00160.0346-0.0060.050854.478420.608529.2563
72.49271.56441.75574.57494.98047.6837-0.143-0.40520.050.24890.4815-0.4433-0.11950.2019-0.27010.16970.1145-0.04760.3263-0.10720.187872.693318.675725.5439
84.7588-0.28661.62124.9463-1.05744.28370.0384-0.25330.16730.01540.2846-0.5190.19240.5152-0.18850.11360.0437-0.00050.1505-0.06580.146367.415827.800723.9468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 124 )A1 - 124
2X-RAY DIFFRACTION2chain 'A' and (resid 125 through 141 )A125 - 141
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 167 )A142 - 167
4X-RAY DIFFRACTION4chain 'A' and (resid 168 through 182 )A168 - 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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