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- PDB-7l0b: Crystal structure of hydroxyacyl glutathione hydrolase (GloB) fro... -

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Basic information

Entry
Database: PDB / ID: 7l0b
TitleCrystal structure of hydroxyacyl glutathione hydrolase (GloB) from Staphylococcus aureus, apoenzyme
ComponentsHydroxyacylglutathione hydrolase
KeywordsHYDROLASE / GloB / esterase
Function / homology
Function and homology information


hydroxyacylglutathione hydrolase / hydroxyacylglutathione hydrolase activity / Hydrolases / hydrolase activity
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Hydroxyacylglutathione hydrolase / Hydroxyacylglutathione hydrolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsMiller, J.J. / Jez, J.M. / Odom John, A.R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI103280 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI123808 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI130584 United States
Citation
Journal: Elife / Year: 2021
Title: Structure-guided microbial targeting of antistaphylococcal prodrugs.
Authors: Miller, J.J. / Shah, I.T. / Hatten, J. / Barekatain, Y. / Mueller, E.A. / Moustafa, A.M. / Edwards, R.L. / Dowd, C.S. / Planet, P.J. / Muller, F.L. / Jez, J.M. / Odom John, A.R.
#1: Journal: Biorxiv / Year: 2020
Title: Structure-guided microbial targeting of antistaphylococcal prodrugs
Authors: Miller, J.J. / Shah, I.T. / Hatten, J. / Barekatain, Y. / Mueller, E.A. / Moustafa, A.M. / Edwaards, R.L. / Dowd, C.S. / Planet, P.J. / Muller, F.L. / Jez, J.M. / Odom John, A.R.
History
DepositionDec 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxyacylglutathione hydrolase
B: Hydroxyacylglutathione hydrolase
C: Hydroxyacylglutathione hydrolase
D: Hydroxyacylglutathione hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,84816
Polymers94,9414
Non-polymers90812
Water7,476415
1
A: Hydroxyacylglutathione hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9624
Polymers23,7351
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hydroxyacylglutathione hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9624
Polymers23,7351
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Hydroxyacylglutathione hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9624
Polymers23,7351
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Hydroxyacylglutathione hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9624
Polymers23,7351
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.672, 44.757, 105.041
Angle α, β, γ (deg.)90.000, 96.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hydroxyacylglutathione hydrolase / MBL fold metallo-hydrolase / Metallo-beta-lactamase superfamily protein / Putative metallo-hydrolase


Mass: 23735.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: W8UAH2, UniProt: A0A0D1GCF8*PLUS, hydroxyacylglutathione hydrolase, Hydrolases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 2 uL hanging drops containing a 1:1 mixture of protein (8 mg/mL) and crystallization buffer (0.1 M imidazole pH 6.9, 0.2 M ammonium sulfate, 0.1 M calcium chloride, and 21% PEG 8k)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 195660 / % possible obs: 98.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.05 / Rrim(I) all: 0.119 / Χ2: 1.072 / Net I/σ(I): 4.8 / Num. measured all: 537795
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.939 / Num. unique obs: 5122 / CC1/2: 0.993 / Rpim(I) all: 0.041 / Rrim(I) all: 0.098 / Χ2: 2.994 / % possible all: 88.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZWR

2zwr


Resolution: 1.65→47.96 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 9763 4.99 %
Rwork0.227 185897 -
obs0.228 195660 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.31 Å2 / Biso mean: 39.65 Å2 / Biso min: 17.6 Å2
Refinement stepCycle: final / Resolution: 1.65→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6260 0 28 415 6703
Biso mean--47.54 44.47 -
Num. residues----795
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.670.50452550.42444568482371
1.67-1.690.43452880.41265267555583
1.69-1.710.46412500.39665929617990
1.71-1.730.38833240.38836005632993
1.73-1.750.39183180.37996169648796
1.75-1.780.37913310.34716245657697
1.78-1.80.33743200.32456316663698
1.8-1.830.33223520.31096224657698
1.83-1.860.31593710.296344671598
1.86-1.890.31223090.27856318662798
1.89-1.920.2913050.27476305661098
1.92-1.960.27923560.25856249660597
1.96-1.990.29093580.24446362672099
1.99-2.040.26253100.24196459676999
2.04-2.080.29463370.2386272660999
2.08-2.130.26993180.22826429674798
2.13-2.180.2563310.23096248657998
2.18-2.240.22413490.21486387673698
2.24-2.310.25753330.2176214654798
2.31-2.380.24853490.22076249659897
2.38-2.470.22973290.21856426675599
2.47-2.560.26143320.21116281661399
2.56-2.680.22872880.21836439672798
2.68-2.820.26133300.2266377670798
2.82-30.23023270.22266327665498
3-3.230.26423690.21716298666798
3.23-3.560.24263050.20286401670699
3.56-4.070.21723300.19476401673198
4.07-5.130.18523260.1836207653397
5.13-100.23353630.22046181654496

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