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- PDB-6z25: Acylenzyme complex of ceftazidime bound to deacylation mutant KPC... -

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Basic information

Entry
Database: PDB / ID: 6z25
TitleAcylenzyme complex of ceftazidime bound to deacylation mutant KPC-4 (E166Q)
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / unliganded beta-lactamase / 3-layer alpha-beta-alpha sandwich / part of the DD-peptidase and beta-lactamase superfamily.
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACYLATED CEFTAZIDIME / beta-lactamase / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsTooke, C.L. / Hinchliffe, P. / Spencer, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/T016035/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J014400/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Natural variants modify Klebsiella pneumoniae carbapenemase (KPC) acyl-enzyme conformational dynamics to extend antibiotic resistance.
Authors: Tooke, C.L. / Hinchliffe, P. / Bonomo, R.A. / Schofield, C.J. / Mulholland, A.J. / Spencer, J.
History
DepositionMay 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: 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 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,14211
Polymers30,8241
Non-polymers1,31810
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-57 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.230, 77.265, 55.741
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-461-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 30823.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaKPC-4, blaKPC-2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1PL86, UniProt: Q9F663*PLUS, beta-lactamase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CAZ / ACYLATED CEFTAZIDIME


Mass: 469.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N5O7S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 1.8 M ammonium sulphate, 5% ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.81001 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81001 Å / Relative weight: 1
ReflectionResolution: 1.24→55.74 Å / Num. obs: 73167 / % possible obs: 96.8 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.038 / Rrim(I) all: 0.141 / Net I/σ(I): 9.4
Reflection shellResolution: 1.24→1.26 Å / Rmerge(I) obs: 2.827 / Mean I/σ(I) obs: 1 / Num. unique obs: 3483 / CC1/2: 0.747 / Rpim(I) all: 1.114 / Rrim(I) all: 3.04 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QWE

6qwe


Resolution: 1.24→55.741 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.75
RfactorNum. reflection% reflection
Rfree0.1704 3675 5.03 %
Rwork0.1439 --
obs0.1453 73046 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.75 Å2 / Biso mean: 21.9467 Å2 / Biso min: 10 Å2
Refinement stepCycle: final / Resolution: 1.24→55.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 189 239 2445
Biso mean--41.53 35.8 -
Num. residues----270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.24-1.25630.34311400.2938254596
1.2563-1.27350.31821490.265258597
1.2735-1.29170.32091390.2527260097
1.2917-1.3110.24331420.2444259797
1.311-1.33150.27291600.2285258797
1.3315-1.35330.21741520.2124257697
1.3533-1.37670.24531410.216263497
1.3767-1.40170.2191320.2036261997
1.4017-1.42870.24761260.1861266398
1.4287-1.45780.21911130.1702264598
1.4578-1.48950.17471140.157267598
1.4895-1.52420.16071470.1436263398
1.5242-1.56230.18511370.1337266198
1.5623-1.60460.17771260.1279265698
1.6046-1.65180.16481460.1275265398
1.6518-1.70510.16241430.1303266899
1.7051-1.7660.18091200.1329268498
1.766-1.83680.19941430.13268999
1.8368-1.92040.15051530.1197268299
1.9204-2.02160.12571450.1169268699
2.0216-2.14830.14441580.1181270399
2.1483-2.31410.13281490.1116271199
2.3141-2.5470.15621480.12092732100
2.547-2.91560.12721570.12212752100
2.9156-3.67320.1751260.13682821100
3.6732-55.7410.17461690.1622914100

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