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

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Basic information

Entry
Database: PDB / ID: 6dgu
TitlePER-2 class A extended-spectrum beta-lactamase crystal structure at 2.69 Angstrom resolution
ComponentsBeta-lactamase
KeywordsHYDROLASE / penicilloil-serine-transferase / antibiotic resistance
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
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.691 Å
AuthorsPower, P. / Ruggiero, M. / Gutkind, G. / Bonomo, R. / Klinke, S.
Funding support Argentina, 2items
OrganizationGrant numberCountry
National Agency for the Promotion of Science and Technology of Argentina (ANPCyT)PICT-2004-0457 Argentina
Fund for Scientific and Technological Research (FONCYT)PPL-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
DepositionMay 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: 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 11, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Beta-lactamase
A: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)122,6804
Polymers122,6804
Non-polymers00
Water3,135174
1
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)30,6701
Polymers30,6701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)30,6701
Polymers30,6701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)30,6701
Polymers30,6701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)30,6701
Polymers30,6701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.370, 82.580, 174.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 28 through 293)
21(chain B and resid 28 through 293)
31(chain C and resid 28 through 293)
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 28 - 293 / Label seq-ID: 3 - 274

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 28 through 293)AB
2(chain B and resid 28 through 293)BA
3(chain C and resid 28 through 293)CC
4chain DDD

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Components

#1: Protein
Beta-lactamase /


Mass: 30670.041 Da / Num. of mol.: 4 / Fragment: residues 28-308
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 49.93 %
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: 2.691→41.29 Å / Num. obs: 32951 / % possible obs: 97.28 % / Redundancy: 5.46 % / Biso Wilson estimate: 27.22 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.164 / Rrim(I) all: 0.18 / Net I/σ(I): 9.74
Reflection shellResolution: 2.691→2.85 Å / Redundancy: 5.46 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.63 / Num. unique obs: 4944 / CC1/2: 0.78 / Rrim(I) all: 0.5 / % possible all: 91.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHENIX1.12-2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2O

4d2o


Resolution: 2.691→41.29 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 35.01
RfactorNum. reflection% reflection
Rfree0.3396 1980 6.01 %
Rwork0.267 --
obs0.2713 32951 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 40.03 Å2 / Biso mean: 23.9005 Å2 / Biso min: 2.57 Å2
Refinement stepCycle: final / Resolution: 2.691→41.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8442 0 0 174 8616
Biso mean---22.24 -
Num. residues----1098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018597
X-RAY DIFFRACTIONf_angle_d1.35711677
X-RAY DIFFRACTIONf_chiral_restr0.081368
X-RAY DIFFRACTIONf_plane_restr0.011501
X-RAY DIFFRACTIONf_dihedral_angle_d4.8585203
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5086X-RAY DIFFRACTION12.193TORSIONAL
12B5086X-RAY DIFFRACTION12.193TORSIONAL
13C5086X-RAY DIFFRACTION12.193TORSIONAL
14D5086X-RAY DIFFRACTION12.193TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6912-2.75850.46081230.41421872199583
2.7585-2.83310.40261360.3432206234298
2.8331-2.91640.35731400.31912183232398
2.9164-3.01050.38971430.30032173231698
3.0105-3.11810.36981440.29112194233898
3.1181-3.24290.39121450.28512229237498
3.2429-3.39040.35491380.27222223236198
3.3904-3.5690.38761410.26962213235498
3.569-3.79250.36291450.26232236238198
3.7925-4.08510.33221380.25142246238499
4.0851-4.49570.31191450.23732260240599
4.4957-5.14520.28351440.22962285242999
5.1452-6.47840.32581460.25612301244799
6.4784-41.29480.24321520.21262350250296

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