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- PDB-9enx: Enmetazobactam-Derived GES-1 Acyl-Enzyme -

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Basic information

Entry
Database: PDB / ID: 9enx
TitleEnmetazobactam-Derived GES-1 Acyl-Enzyme
Componentsbeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase / antibiotic resistance / enzyme / inhibitor / complex / ligand
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Enmetazobactam derived trans-enamine adduct. / Beta-lactamase GES-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsBeer, M. / Hinchliffe, P. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008741/10 United Kingdom
CitationJournal: To Be Published
Title: Enmetazobactam-Derived GES-1 Acyl-Enzyme
Authors: Beer, M. / Hinchliffe, P. / Spencer, J.
History
DepositionMar 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-lactamase
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4379
Polymers62,9392
Non-polymers1,4987
Water11,007611
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3966
Polymers31,4701
Non-polymers9265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0413
Polymers31,4701
Non-polymers5722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.804, 81.034, 71.551
Angle α, β, γ (deg.)90.000, 101.810, 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 beta-lactamase


Mass: 31469.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ges-1, blaGES-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KJY7, beta-lactamase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-M9W / Enmetazobactam derived trans-enamine adduct / (2S,3S)-3-methyl-4-(3-methyl-1,2,3-triazol-3-ium-1-yl)-2-[[(E)-3-oxidanylideneprop-1-enyl]amino]-3-sulfino-butanoic acid


Mass: 333.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N4O6S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.93 Å3/Da / Density % sol: 36.26 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 20 mM HEPES pH 7.6, 10% PEG8000, 10% PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.73379 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.73379 Å / Relative weight: 1
ReflectionResolution: 1.23→81.03 Å / Num. obs: 138378 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.69 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.045 / Net I/σ(I): 8.1
Reflection shellResolution: 1.23→1.25 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 6614 / CC1/2: 0.314 / Rpim(I) all: 1.151

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→70.04 Å / SU ML: 0.2163 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.28
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1935 6783 5 %
Rwork0.1519 128782 -
obs0.1539 135565 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.06 Å2
Refinement stepCycle: LAST / Resolution: 1.23→70.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4039 0 96 611 4746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794279
X-RAY DIFFRACTIONf_angle_d0.95935805
X-RAY DIFFRACTIONf_chiral_restr0.0738657
X-RAY DIFFRACTIONf_plane_restr0.0095747
X-RAY DIFFRACTIONf_dihedral_angle_d13.94091622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.240.41811740.4113188X-RAY DIFFRACTION73.31
1.24-1.260.42412100.41423795X-RAY DIFFRACTION85.82
1.26-1.270.40571860.40553850X-RAY DIFFRACTION88.28
1.27-1.290.42832220.3984082X-RAY DIFFRACTION93.5
1.29-1.310.41582090.38764282X-RAY DIFFRACTION97.82
1.31-1.320.37292460.37324272X-RAY DIFFRACTION97.96
1.32-1.340.36272070.3654330X-RAY DIFFRACTION99
1.34-1.360.3792370.34114367X-RAY DIFFRACTION99.72
1.36-1.380.35092300.3244421X-RAY DIFFRACTION99.83
1.38-1.410.34452460.2994322X-RAY DIFFRACTION99.83
1.41-1.430.30772590.27784359X-RAY DIFFRACTION99.74
1.43-1.460.2962280.25184330X-RAY DIFFRACTION99.74
1.46-1.490.27162200.23824394X-RAY DIFFRACTION99.89
1.49-1.520.27862520.20894353X-RAY DIFFRACTION99.89
1.52-1.550.24042220.19344372X-RAY DIFFRACTION99.96
1.55-1.580.24172210.17964429X-RAY DIFFRACTION100
1.58-1.620.19842250.16614355X-RAY DIFFRACTION99.91
1.62-1.670.21312450.15434374X-RAY DIFFRACTION99.87
1.67-1.720.21792430.14574387X-RAY DIFFRACTION99.87
1.72-1.770.19872270.13754357X-RAY DIFFRACTION99.93
1.77-1.840.19232040.12894419X-RAY DIFFRACTION99.96
1.84-1.910.18572110.1294401X-RAY DIFFRACTION100
1.91-20.18372200.12314409X-RAY DIFFRACTION99.98
2-2.10.14472540.10964382X-RAY DIFFRACTION99.98
2.1-2.230.16322160.10754432X-RAY DIFFRACTION99.98
2.23-2.410.15372380.1114377X-RAY DIFFRACTION100
2.41-2.650.15112350.10944396X-RAY DIFFRACTION100
2.65-3.030.1542370.11224413X-RAY DIFFRACTION100
3.03-3.820.1442360.10784440X-RAY DIFFRACTION100
3.82-70.040.15442230.12474494X-RAY DIFFRACTION99.94

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