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- PDB-8v9h: GES-5-NA-1-157 complex -

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Basic information

Entry
Database: PDB / ID: 8v9h
TitleGES-5-NA-1-157 complex
Componentsbeta-lactamase
KeywordsHYDROLASE / class A beta-lactamase / carbapenemase / meropenem / antibiotic resistance
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / extracellular region
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
IODIDE ION / Chem-Y33 / Beta-lactamase GES-5
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSmith, C.A. / Stewart, N.K. / Vakulenko, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI155723 United States
CitationJournal: Acs Infect Dis. / Year: 2024
Title: Restricted Rotational Flexibility of the C5 alpha-Methyl-Substituted Carbapenem NA-1-157 Leads to Potent Inhibition of the GES-5 Carbapenemase.
Authors: Stewart, N.K. / Toth, M. / Quan, P. / Beer, M. / Buynak, J.D. / Smith, C.A. / Vakulenko, S.B.
History
DepositionDec 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 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: beta-lactamase
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,16519
Polymers62,4452
Non-polymers1,72017
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-75 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.727, 80.381, 87.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein beta-lactamase


Mass: 31222.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaGES-5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09HD0

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Non-polymers , 6 types, 398 molecules

#2: Chemical ChemComp-Y33 / (5R)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid


Mass: 401.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 277 K / Method: batch mode
Details: Crystallized spontaneously from 20 mM HEPES. Protein concentration 15 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→38.5 Å / Num. obs: 87364 / % possible obs: 99.9 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rpim(I) all: 0.031 / Rrim(I) all: 0.094 / Net I/σ(I): 15.2
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4276 / CC1/2: 0.803 / Rpim(I) all: 0.416

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→38.5 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1917 4670 5.35 %
Rwork0.1598 --
obs0.1614 87357 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4059 0 79 381 4519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064255
X-RAY DIFFRACTIONf_angle_d1.0875771
X-RAY DIFFRACTIONf_dihedral_angle_d10.674636
X-RAY DIFFRACTIONf_chiral_restr0.057663
X-RAY DIFFRACTIONf_plane_restr0.01754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.3331590.28222751X-RAY DIFFRACTION100
1.52-1.530.30161600.22292705X-RAY DIFFRACTION100
1.53-1.550.22461570.19982726X-RAY DIFFRACTION100
1.55-1.570.26761560.19592745X-RAY DIFFRACTION100
1.57-1.590.26151670.18712682X-RAY DIFFRACTION100
1.59-1.620.23781590.1732701X-RAY DIFFRACTION100
1.62-1.640.20251540.1612745X-RAY DIFFRACTION100
1.64-1.660.19261630.15332720X-RAY DIFFRACTION100
1.66-1.690.23381610.15462732X-RAY DIFFRACTION100
1.69-1.720.21641550.14922708X-RAY DIFFRACTION100
1.72-1.750.19781840.15072731X-RAY DIFFRACTION100
1.75-1.780.20521370.14822696X-RAY DIFFRACTION100
1.78-1.810.18812010.1472708X-RAY DIFFRACTION100
1.81-1.850.20891800.15492714X-RAY DIFFRACTION100
1.85-1.890.1961560.152742X-RAY DIFFRACTION100
1.89-1.930.19881370.13532734X-RAY DIFFRACTION100
1.93-1.980.18811520.14012760X-RAY DIFFRACTION100
1.98-2.040.19681420.13862749X-RAY DIFFRACTION100
2.04-2.10.18671390.14052764X-RAY DIFFRACTION100
2.1-2.160.17561300.14362786X-RAY DIFFRACTION100
2.16-2.240.15461350.14442776X-RAY DIFFRACTION100
2.24-2.330.20371430.1512767X-RAY DIFFRACTION100
2.33-2.440.19121610.1622768X-RAY DIFFRACTION100
2.44-2.560.17951420.16312765X-RAY DIFFRACTION100
2.56-2.730.1871780.16042759X-RAY DIFFRACTION100
2.73-2.940.20211890.17492750X-RAY DIFFRACTION100
2.94-3.230.21021400.17472822X-RAY DIFFRACTION100
3.23-3.70.1936850.16722879X-RAY DIFFRACTION100
3.7-4.660.15421780.14612827X-RAY DIFFRACTION100
4.66-38.50.17911700.16542975X-RAY DIFFRACTION100

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