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- PDB-6d3g: PER-2 class A extended-spectrum beta-lactamase crystal structure ... -

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Basic information

Entry
Database: PDB / ID: 6d3g
TitlePER-2 class A extended-spectrum beta-lactamase crystal structure in complex with avibactam at 2.4 Angstrom resolution
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / DBO / penicilloil-serine-transferase / antibiotic resistance / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
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 active site / Beta-lactamase class-A active site. / 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
Chem-NXL / Beta-lactamase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 Å
AuthorsPower, P. / Ruggiero, M. / Gutkind, G. / Bonomo, R. / Klinke, S.
Funding support Argentina, 2items
OrganizationGrant numberCountry
ANPCYTPICT-2004-0457 Argentina
FONCYTPPL-2011-2-0003 Argentina
CitationJournal: Antimicrob.Agents Chemother. / Year: 2019
Title: Structural Insights into the Inhibition of the Extended-Spectrum beta-Lactamase PER-2 by Avibactam.
Authors: Ruggiero, M. / Papp-Wallace, K.M. / Brunetti, F. / Barnes, M.D. / Bonomo, R.A. / Gutkind, G. / Klinke, S. / Power, P.
History
DepositionApr 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,0899
Polymers123,8254
Non-polymers1,2635
Water1,33374
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2242
Polymers30,9561
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4183
Polymers30,9561
Non-polymers4612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2242
Polymers30,9561
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2242
Polymers30,9561
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.160, 85.840, 161.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Beta-lactamase


Mass: 30956.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: blaPER-2 / Plasmid: pET28/PER-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2RP81, beta-lactamase
#2: Chemical
ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 6000, 0.05 M imidazole pH=8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 11, 2016
Details: CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.398→48.17 Å / Num. obs: 46410 / % possible obs: 99.76 % / Redundancy: 6.65 % / Biso Wilson estimate: 55.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.092 / Net I/σ(I): 13.73
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 6.65 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 7289 / CC1/2: 0.746 / Rrim(I) all: 1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHENIX1.12-2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2O

4d2o


Resolution: 2.398→48.17 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.31
RfactorNum. reflection% reflection
Rfree0.2525 2321 5 %
Rwork0.2059 --
obs0.2083 46400 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 65.73 Å2
Refinement stepCycle: LAST / Resolution: 2.398→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8546 0 81 74 8701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138791
X-RAY DIFFRACTIONf_angle_d1.55911934
X-RAY DIFFRACTIONf_dihedral_angle_d13.9725299
X-RAY DIFFRACTIONf_chiral_restr0.0951396
X-RAY DIFFRACTIONf_plane_restr0.0111528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.398-2.44690.35131290.29622450X-RAY DIFFRACTION97
2.4469-2.50010.34541350.27462558X-RAY DIFFRACTION100
2.5001-2.55830.36061360.2712586X-RAY DIFFRACTION100
2.5583-2.62230.30791340.25552551X-RAY DIFFRACTION100
2.6223-2.69320.31731350.24842564X-RAY DIFFRACTION100
2.6932-2.77240.29011360.25192575X-RAY DIFFRACTION100
2.7724-2.86190.37391350.26312568X-RAY DIFFRACTION100
2.8619-2.96420.32181360.27672579X-RAY DIFFRACTION100
2.9642-3.08280.33951360.27692583X-RAY DIFFRACTION100
3.0828-3.22310.30331350.25592565X-RAY DIFFRACTION100
3.2231-3.3930.32991360.23982586X-RAY DIFFRACTION100
3.393-3.60550.30841370.22152598X-RAY DIFFRACTION100
3.6055-3.88380.24531370.20292618X-RAY DIFFRACTION100
3.8838-4.27440.20081380.17162611X-RAY DIFFRACTION100
4.2744-4.89240.18521380.16192626X-RAY DIFFRACTION100
4.8924-6.16190.21111410.18362668X-RAY DIFFRACTION100
6.1619-48.180.19551470.16282793X-RAY DIFFRACTION100

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