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- PDB-9eny: Tazobactam-Derived GES-1 Acyl-Enzyme -

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Basic information

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


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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
: / MALONALDEHYDE / Beta-lactamase GES-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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: Tazobactam-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)63,8607
Polymers62,9392
Non-polymers9215
Water11,061614
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7803
Polymers31,4701
Non-polymers3102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0804
Polymers31,4701
Non-polymers6113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.950, 80.710, 104.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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-MDD / MALONALDEHYDE


Mass: 72.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1H57 / tazobactam (2S,3S,5R)


Mass: 300.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.02 M citric acid, 0.08 M Bis-Tris propane, 10 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.3→63.89 Å / Num. obs: 146232 / % possible obs: 92.5 % / Redundancy: 12.3 % / Biso Wilson estimate: 25.38 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.039 / Net I/σ(I): 5.8
Reflection shellResolution: 1.3→1.32 Å / Mean I/σ(I) obs: 0.1 / Num. unique obs: 4162 / CC1/2: 0.269 / Rpim(I) all: 1.624

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→61.45 Å / SU ML: 0.2207 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9887
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1946 5488 5.01 %
Rwork0.1516 104013 -
obs0.1537 109501 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.21 Å2
Refinement stepCycle: LAST / Resolution: 1.47→61.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4064 0 60 614 4738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00844231
X-RAY DIFFRACTIONf_angle_d0.97715727
X-RAY DIFFRACTIONf_chiral_restr0.0736647
X-RAY DIFFRACTIONf_plane_restr0.0102744
X-RAY DIFFRACTIONf_dihedral_angle_d13.63251593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.490.40591760.43493432X-RAY DIFFRACTION99.48
1.49-1.50.43841960.40923374X-RAY DIFFRACTION99.61
1.5-1.520.40641910.37413464X-RAY DIFFRACTION99.56
1.52-1.540.37471790.3523394X-RAY DIFFRACTION99.8
1.54-1.560.36141750.32143443X-RAY DIFFRACTION99.89
1.56-1.580.3311660.3063447X-RAY DIFFRACTION99.78
1.58-1.610.32511980.26643404X-RAY DIFFRACTION99.81
1.61-1.630.25781870.24483421X-RAY DIFFRACTION99.83
1.63-1.660.30631860.22423485X-RAY DIFFRACTION99.81
1.66-1.680.28221750.2163406X-RAY DIFFRACTION99.69
1.68-1.710.28171720.21313426X-RAY DIFFRACTION99.83
1.71-1.740.27022130.19923384X-RAY DIFFRACTION99.56
1.74-1.780.26591950.18173420X-RAY DIFFRACTION99.67
1.78-1.810.20961730.17573469X-RAY DIFFRACTION99.56
1.81-1.850.21552020.15613419X-RAY DIFFRACTION99.92
1.85-1.90.21661880.14093450X-RAY DIFFRACTION99.97
1.9-1.940.19241860.14143459X-RAY DIFFRACTION99.97
1.94-20.19841910.12813430X-RAY DIFFRACTION99.97
2-2.050.17631620.11873524X-RAY DIFFRACTION99.97
2.05-2.120.16421760.12093448X-RAY DIFFRACTION99.94
2.12-2.20.18071580.12653491X-RAY DIFFRACTION100
2.2-2.280.19161740.12453468X-RAY DIFFRACTION100
2.28-2.390.18341830.1253493X-RAY DIFFRACTION99.84
2.39-2.510.17931610.12653502X-RAY DIFFRACTION100
2.51-2.670.18541520.12553522X-RAY DIFFRACTION99.89
2.67-2.880.17491940.13433512X-RAY DIFFRACTION99.97
2.88-3.170.16861580.14143550X-RAY DIFFRACTION100
3.17-3.630.172200.14633494X-RAY DIFFRACTION99.97
3.63-4.570.16531880.12623573X-RAY DIFFRACTION99.87
4.57-61.450.19572130.16813709X-RAY DIFFRACTION99.82

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