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- PDB-9bzq: Structure of Class A Beta-lactamase from Bordetella bronchiseptic... -

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Basic information

Entry
Database: PDB / ID: 9bzq
TitleStructure of Class A Beta-lactamase from Bordetella bronchiseptica RB50 in a complex with Avibactam
Componentsclass A Beta-lactamase, PenP superfamily
KeywordsHYDROLASE / lactamase / serine hydrolase / PenP / CSBID / Center for Structural Biology of Infectious Diseases / Avibactam
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
FORMIC ACID / Chem-NXL / SUCCINIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesBordetella bronchiseptica RB50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsMaltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Structure of Class A Beta-lactamase from Bordetella bronchiseptica RB50 in a complex with Avibactam
Authors: Maltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A.
History
DepositionMay 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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: class A Beta-lactamase, PenP superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4085
Polymers28,9141
Non-polymers4934
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.223, 79.463, 42.939
Angle α, β, γ (deg.)90.000, 108.170, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein class A Beta-lactamase, PenP superfamily


Mass: 28914.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica RB50 (bacteria)
Gene: BB2049 / Plasmid: p53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A0H3LUA9, beta-lactamase

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Non-polymers , 5 types, 311 molecules

#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.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Succinic acid pH 7.0; 15% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97935 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 39292 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 7.6 Å2 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.016 / Net I/σ(I): 48.8
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.079 / Num. unique obs: 1936 / CC1/2: 0.992 / Rpim(I) all: 0.04 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→26.01 Å / SU ML: 0.1089 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 13.6027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1547 1945 4.95 %
Rwork0.124 37321 -
obs0.1256 39266 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.19 Å2
Refinement stepCycle: LAST / Resolution: 1.47→26.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 32 307 2363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00482164
X-RAY DIFFRACTIONf_angle_d0.82642938
X-RAY DIFFRACTIONf_chiral_restr0.0691324
X-RAY DIFFRACTIONf_plane_restr0.0125402
X-RAY DIFFRACTIONf_dihedral_angle_d12.5508816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.510.16591530.09242655X-RAY DIFFRACTION98.87
1.51-1.550.14111340.0882620X-RAY DIFFRACTION100
1.55-1.590.13851350.0952679X-RAY DIFFRACTION100
1.59-1.640.15711240.10022689X-RAY DIFFRACTION100
1.64-1.70.15251540.10252623X-RAY DIFFRACTION100
1.7-1.770.15331360.11192650X-RAY DIFFRACTION100
1.77-1.850.16421200.10872678X-RAY DIFFRACTION100
1.85-1.950.14651580.12092682X-RAY DIFFRACTION99.96
1.95-2.070.1711250.12472650X-RAY DIFFRACTION100
2.07-2.230.15011400.12162688X-RAY DIFFRACTION100
2.23-2.450.15781400.13082648X-RAY DIFFRACTION100
2.45-2.810.15661350.14442694X-RAY DIFFRACTION100
2.81-3.540.16451490.1432666X-RAY DIFFRACTION100
3.54-26.010.14531420.13622699X-RAY DIFFRACTION99.16

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