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- PDB-9bzn: High resolution structure of class A Beta-lactamase from Bordetel... -

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Basic information

Entry
Database: PDB / ID: 9bzn
TitleHigh resolution structure of class A Beta-lactamase from Bordetella bronchiseptica RB50
Componentsclass A Beta-lactamase, PenP superfamily
KeywordsHYDROLASE / lactamase / serine hydrolase / PenP / CSBID / Center for Structural Biology of Infectious Diseases / Structural Genomics
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 / Beta-lactamase
Similarity search - Component
Biological speciesBordetella bronchiseptica RB50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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: High resolution structure of class A Beta-lactamase from Bordetella bronchiseptica RB50
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: class A Beta-lactamase, PenP superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0573
Polymers28,9141
Non-polymers1422
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.064, 79.549, 42.891
Angle α, β, γ (deg.)90.000, 108.280, 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

#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
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Succinic acid pH 7.0; 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 97955 / % possible obs: 91.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 8.79 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.033 / Net I/σ(I): 23.85
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 5.24 / Num. unique obs: 3838 / CC1/2: 0.942 / Rpim(I) all: 0.137 / % possible all: 71.9

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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: 1.05→31.45 Å / SU ML: 0.0719 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 12.0019
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1409 4910 5.01 %
Rwork0.1273 93000 -
obs0.128 97910 91.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.24 Å2
Refinement stepCycle: LAST / Resolution: 1.05→31.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 8 336 2367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422185
X-RAY DIFFRACTIONf_angle_d0.83522979
X-RAY DIFFRACTIONf_chiral_restr0.0739330
X-RAY DIFFRACTIONf_plane_restr0.0106407
X-RAY DIFFRACTIONf_dihedral_angle_d11.6259817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.060.19411460.16642665X-RAY DIFFRACTION79.43
1.06-1.080.17451590.14032982X-RAY DIFFRACTION89.21
1.08-1.090.14851580.1353029X-RAY DIFFRACTION89.93
1.09-1.10.16231450.12573049X-RAY DIFFRACTION90.3
1.1-1.120.13891480.11583032X-RAY DIFFRACTION90.44
1.12-1.130.14041670.11653063X-RAY DIFFRACTION89.95
1.13-1.150.12941490.11232844X-RAY DIFFRACTION85.54
1.15-1.170.13351670.11023073X-RAY DIFFRACTION90.55
1.17-1.180.12621500.11153041X-RAY DIFFRACTION91.41
1.18-1.20.14151720.11143109X-RAY DIFFRACTION91.65
1.2-1.220.12831690.11313078X-RAY DIFFRACTION92.14
1.22-1.250.13021780.10643109X-RAY DIFFRACTION92.18
1.25-1.270.13661470.10953072X-RAY DIFFRACTION92.16
1.27-1.30.12091480.10873049X-RAY DIFFRACTION89.13
1.3-1.320.13431510.10762988X-RAY DIFFRACTION89.13
1.32-1.350.11891630.10813138X-RAY DIFFRACTION93.49
1.35-1.390.12991730.10883180X-RAY DIFFRACTION93.45
1.39-1.430.14471720.11243122X-RAY DIFFRACTION93.55
1.43-1.470.12921680.11063177X-RAY DIFFRACTION94.54
1.47-1.520.12521750.10463171X-RAY DIFFRACTION94.2
1.52-1.570.13861580.10973069X-RAY DIFFRACTION90.39
1.57-1.630.11771740.11893070X-RAY DIFFRACTION91.64
1.63-1.710.15071970.11963238X-RAY DIFFRACTION96.54
1.71-1.80.14941750.12693261X-RAY DIFFRACTION96.49
1.8-1.910.14911590.13333257X-RAY DIFFRACTION96.31
1.91-2.060.1571870.13293231X-RAY DIFFRACTION95.98
2.06-2.260.13891530.13233036X-RAY DIFFRACTION89.23
2.26-2.590.1381800.13993321X-RAY DIFFRACTION98.12
2.59-3.260.14061570.1473341X-RAY DIFFRACTION97.85
3.26-31.450.14661650.13663205X-RAY DIFFRACTION93.15

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