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- PDB-8ewo: Crystal structure of putative glyoxylase II from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 8ewo
TitleCrystal structure of putative glyoxylase II from Pseudomonas aeruginosa
ComponentsPA1813
KeywordsHYDROLASE / metallo-beta-lactamase / metal-ion-binding / glyoxalase II (hydroxyacylglutathione hydrolase) / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology
Function and homology information


hydroxyacylglutathione hydrolase / hydroxyacylglutathione hydrolase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / metal ion binding
Similarity search - Function
: / Hydroxyacylglutathione hydrolase / Hydroxyacylglutathione hydrolase, C-terminal domain / Hydroxyacylglutathione hydrolase, MBL domain / Hydroxyacylglutathione hydrolase C-terminus / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Hydroxyacylglutathione hydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsStogios, P.J. / Skarina, T. / Endres, M. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of putative glyoxylase II from Pseudomonas aeruginosa
Authors: Stogios, P.J.
History
DepositionOct 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Structure summary / Category: audit_author
Revision 1.2Feb 1, 2023Group: Other / Structure summary / Category: pdbx_SG_project / struct_keywords / Item: _struct_keywords.text
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PA1813
B: PA1813
C: PA1813
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,47913
Polymers86,8883
Non-polymers59110
Water6,936385
1
A: PA1813
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2215
Polymers28,9631
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PA1813
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1294
Polymers28,9631
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PA1813
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1294
Polymers28,9631
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.723, 76.608, 75.430
Angle α, β, γ (deg.)90.000, 94.630, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein PA1813


Mass: 28962.781 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA1813 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: Q9I2T1
#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.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M magnesium acetate, 25% PEG3350, cryoprotectant: 6% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.47→30 Å / Num. obs: 28275 / % possible obs: 98.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 28.98 Å2 / CC1/2: 0.825 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.068 / Net I/σ(I): 7.68
Reflection shellResolution: 2.47→2.51 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 1138 / CC1/2: 0.825 / Rpim(I) all: 0.263 / % possible all: 80.4

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XM8

1xm8


Resolution: 2.47→28.71 Å / SU ML: 0.229 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.6085
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1424 5.04 %RANDOM
Rwork0.1791 26831 --
obs0.1812 28255 97.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.52 Å2
Refinement stepCycle: LAST / Resolution: 2.47→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6125 0 15 385 6525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00196283
X-RAY DIFFRACTIONf_angle_d0.47678553
X-RAY DIFFRACTIONf_chiral_restr0.0386945
X-RAY DIFFRACTIONf_plane_restr0.00321133
X-RAY DIFFRACTIONf_dihedral_angle_d16.88542290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.560.29531220.23712230X-RAY DIFFRACTION81.75
2.56-2.660.27991290.24272643X-RAY DIFFRACTION97.71
2.66-2.780.27221410.23162731X-RAY DIFFRACTION99.34
2.78-2.930.28971450.22522724X-RAY DIFFRACTION99.58
2.93-3.110.26171380.20452714X-RAY DIFFRACTION99.72
3.11-3.350.22671430.18822742X-RAY DIFFRACTION99.83
3.35-3.690.22051520.16872751X-RAY DIFFRACTION100
3.69-4.220.17211480.15232727X-RAY DIFFRACTION100
4.22-5.310.17251590.13782747X-RAY DIFFRACTION100
5.32-28.710.19391470.15932822X-RAY DIFFRACTION99.87
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)
12.96327115304-0.06330434764510.6693371814095.023426395940.580660416024.69986676022-0.211927788531-0.4616296859020.4812602463940.3547005887560.01995545037740.618723874606-0.164714329359-0.5053266481070.1897193211330.1865608690410.00902645529727-0.01492927755110.382663682726-0.09734377181320.30811203635329.780940898310.923390951331.1350547447
22.635435409180.773972900444-1.825148730050.3462674053210.04056503991344.089087214430.7546102950250.02321334444920.807450034299-0.0238544399059-0.0301764671650.00677048319165-1.025025006110.50001847335-0.716317223260.703618109574-0.09227873749590.02383623332150.317924185341-0.05085491477340.78286821845141.588886401528.480298754927.6618013707
32.979768356190.97956995234-1.93373072584.66002912413-1.973462156525.04460685456-0.253598092933-0.06122329681490.082894060504-0.0688026810164-0.255387433365-0.493377504325-0.4793165088720.2240911350590.4624901472170.398676825638-0.0748745846026-0.1338461403390.236522734215-0.0243951455680.3873672787344.471365227518.568426130729.4584459389
41.362109707480.134101037792-0.853986445032.804688515260.9983711894293.61217909463-0.069303135592-0.0484409308220.0334629169088-0.0347339244369-0.03471497164920.0375291704444-0.164673938323-0.1376118573130.09816727466040.09380100316790.0400322152842-0.009178725151690.1714561738730.002169213305340.18404716596447.725996853945.05912095996.65590082057
50.744183964152-0.427074832252-0.03411862521841.82588109792-0.150185615322.749116474030.0179624669918-0.0722801936930.0916925683976-0.0837424076627-0.0466729223793-0.0312861128093-0.05425824996350.2110606227140.03598534056170.167747195132-0.028373895989-0.0007971084528860.183146422345-0.0144553341430.21482416874361.176740271740.7081841901-0.539463198418
61.698539346680.8007360600340.2366602418053.13290342883-0.2991386480483.426282725160.03362210662830.0867640508273-0.183090929381-0.0801478829843-0.115629813352-0.1875554259530.09952348214330.2611578553270.1000374818630.1599736524510.04072137202750.02676365422880.153680794519-0.01692149544020.16198004559362.691520813926.1112193447-10.336564606
75.244456872661.667124086840.1359102788292.57653613337-0.08180647557822.109825726560.192472659391-0.709121079833-0.0007330362374560.265413184316-0.217942485851-0.1734321846950.081382033688-0.0391595951090.004074322802460.259510347252-0.0378854569762-0.0458042720550.194546494031-0.01312361426120.19974101949982.928627786446.348536265723.3853283473
83.00407972210.9708661810741.151706612552.686466333611.550194440221.01896513765-0.03782627812680.1112996972360.110047543804-0.07292403681220.008776616363370.0205925489988-0.08691769451910.008256271451510.02774833000240.231006009958-0.03200518354170.0364369557110.1418674775060.01728597444940.16202793538483.037212916243.443955757515.5316767029
93.036953000480.851185327180.1949954237122.58244909472-0.4721799065582.5365599724-0.0508008808778-0.00847767773596-0.351262130344-0.2541620696060.00517808111843-0.2388994070680.3059433280470.3338681109620.04627886983440.229601301590.02779123226080.03638508629240.197492705123-0.01120234052240.26611432595386.792946284431.332470735619.4778711486
101.43488076297-0.00385800447839-0.4795365362161.98083762581-0.06473935606961.01249026289-0.0325900410928-0.22259716179-0.1518057035160.007636736800480.05515083847610.004398361537780.05166967463720.0339692285944-0.02401078220020.167995768389-0.0125760098280.001184823372080.2258307148530.04698531231150.2004493293672.2406503232.277071239330.6092173623
111.744018675572.0367248366-2.16495469715.62524305707-4.545819174598.570804197450.211046308751-0.2112233116530.561560999381.0886623470.1551267811870.558650290204-0.918479191545-0.500544905921-0.3062758273710.3549148474450.03921157217160.04304026695610.325928332505-0.08549933841560.29102822421461.380628660145.164546699635.8525737273
122.627637133720.8534789688940.09772990981473.306267634130.363520639692.287343929280.020114047419-0.249202463550.02920363101840.282499518685-0.08292414835240.4087974405860.220955710988-0.4127438347440.03016595543350.188562837325-0.008887353540620.05502920890480.2865181816950.008561183247170.24898033292562.626113147828.102311658534.2427479549
131.78471394643-0.391056267871-0.117902516533.387572681030.3977628498822.76462587361-0.005034438194340.0285550564282-0.0943080920.163167210235-0.0725767911996-0.1627061893190.02491265295450.231185730160.0774041684530.1082141151010.003362429133130.007207344118840.1756913650690.01776937752170.15720537331841.6425338316-11.802357264421.4470552267
143.88844643261.790281838381.567966428517.20673157859-0.3932610622021.22550198241-0.03802789096310.5936526514810.137573413175-0.625173404938-0.0516383308872-0.282121457366-0.03342397502470.2686251126480.06425707272670.187796255950.01554669672540.07204804469590.302148080141-0.1001855144880.21199278645538.7441415608-4.233330695589.57547889335
151.8659885676-0.1610065836810.5752364208730.8223744815070.7588459739032.40293189665-0.2628381345080.111478781670.219995464979-0.07009153765330.0773932772262-0.128746636572-0.2475051472190.2428996424260.1923221162830.187601388606-0.0467601093054-0.0180698207180.1532585781690.02905264134190.22414268291339.86060173875.404072615719.9646093184
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 173 through 226 )AA173 - 226174 - 227
22chain 'A' and (resid 227 through 243 )AA227 - 243228 - 244
33chain 'A' and (resid 244 through 258 )AA244 - 258245 - 259
44chain 'B' and (resid 1 through 95 )BC1 - 951 - 95
55chain 'B' and (resid 96 through 172 )BC96 - 17296 - 172
66chain 'B' and (resid 173 through 258 )BC173 - 258173 - 258
77chain 'C' and (resid 0 through 29 )CD0 - 291 - 30
88chain 'C' and (resid 30 through 64 )CD30 - 6431 - 65
99chain 'C' and (resid 65 through 116 )CD65 - 11666 - 117
1010chain 'C' and (resid 117 through 187 )CD117 - 187118 - 188
1111chain 'C' and (resid 188 through 202 )CD188 - 202189 - 203
1212chain 'C' and (resid 203 through 258 )CD203 - 258204 - 259
1313chain 'A' and (resid 0 through 95 )AA0 - 951 - 96
1414chain 'A' and (resid 96 through 108 )AA96 - 10897 - 109
1515chain 'A' and (resid 109 through 172 )AA109 - 172110 - 173

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