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- PDB-8qnn: Crystal structure of a Class A beta-lactamase from Nocardia cyria... -

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Basic information

Entry
Database: PDB / ID: 8qnn
TitleCrystal structure of a Class A beta-lactamase from Nocardia cyriacigeorgica
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / drug-resistance / beta-lactam / nocardia
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/transpeptidase-like
Similarity search - Domain/homology
CITRATE ANION / Beta-lactamase
Similarity search - Component
Biological speciesNocardia cyriacigeorgica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsFeuillard, J. / Couston, J. / Benito, Y. / Hodille, E. / Dumitrescu, O. / Blaise, M.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Biochemical and structural characterization of a class A beta-lactamase from Nocardia cyriacigeorgica.
Authors: Feuillard, J. / Couston, J. / Benito, Y. / Hodille, E. / Dumitrescu, O. / Blaise, M.
History
DepositionSep 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3203
Polymers27,9421
Non-polymers3782
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.180, 54.180, 131.860
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-402-

FLC

21A-598-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 27941.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: engineered sequence / Source: (gene. exp.) Nocardia cyriacigeorgica (bacteria) / Strain: clinical strain / Gene: bla / Plasmid: pET champion SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5R8NCK8
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M citric acid pH3.5, 10 % PEG 6000 and 6% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.25→43.95 Å / Num. obs: 63063 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 17.77 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.078 / Net I/σ(I): 12
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 8.8 % / Num. unique obs: 27178 / CC1/2: 0.28 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5008refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→43.95 Å / SU ML: 0.1444 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.5543
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1745 2002 3.18 %
Rwork0.1416 60992 -
obs0.1426 62994 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.54 Å2
Refinement stepCycle: LAST / Resolution: 1.25→43.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 26 210 2175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742023
X-RAY DIFFRACTIONf_angle_d0.93582771
X-RAY DIFFRACTIONf_chiral_restr0.0739323
X-RAY DIFFRACTIONf_plane_restr0.0098369
X-RAY DIFFRACTIONf_dihedral_angle_d11.4784722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.3051410.25464320X-RAY DIFFRACTION100
1.28-1.320.28421430.22854288X-RAY DIFFRACTION100
1.32-1.350.30071390.2414298X-RAY DIFFRACTION99.98
1.35-1.40.28551420.22274283X-RAY DIFFRACTION100
1.4-1.450.25971430.19074281X-RAY DIFFRACTION99.95
1.45-1.510.18921440.13924339X-RAY DIFFRACTION100
1.51-1.570.1821380.1324306X-RAY DIFFRACTION100
1.57-1.660.19661410.12134335X-RAY DIFFRACTION100
1.66-1.760.17911430.14564348X-RAY DIFFRACTION100
1.76-1.90.15631410.1164337X-RAY DIFFRACTION100
1.9-2.090.15111450.13894388X-RAY DIFFRACTION99.98
2.09-2.390.14621440.12864383X-RAY DIFFRACTION100
2.39-3.010.16621420.13724456X-RAY DIFFRACTION99.96
3.01-43.950.16871560.13734630X-RAY DIFFRACTION99.75

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