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- PDB-7ddm: Crystal Structure of PenA39 beta-Lactamase -

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Basic information

Entry
Database: PDB / ID: 7ddm
TitleCrystal Structure of PenA39 beta-Lactamase
Components
  • ALA-ALA-ARG-ASP-ALA-ALA-VAL-SER-ASP-ALA-ALA-ALA
  • Beta-lactamase
KeywordsHYDROLASE / beta-lactamase
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
ACETATE ION / Beta-lactamase
Similarity search - Component
Biological speciesBurkholderia multivorans CGD2 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsNukaga, M. / Hoshino, T. / Papp-Wallace, K.M.
Funding support Japan, United States, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K07484 Japan
Veterans Affairs Biomedical Laboratory Research and Development ServiceBX002872 United States
Cystic Fibrosis FoundationLIPUMA13I0 and LIPUMA15P0 United States
CitationJournal: To Be Published
Title: Frameshift mutations in genes encoding PBP3 and PBP4 trigger an unusual, extreme beta-lactam resistance phenotype in Burkholderia multivorans
Authors: Nukaga, M. / Becka, S.A. / Zeiser, E.T. / Hoshino, Y. / LiPuma, J.J. / Papp-Wallace, K.M.
History
DepositionOct 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
E: ALA-ALA-ARG-ASP-ALA-ALA-VAL-SER-ASP-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,43910
Polymers32,6712
Non-polymers7688
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-32 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.519, 65.519, 51.421
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein Beta-lactamase


Mass: 31581.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans CGD2 (bacteria)
Gene: BURMUCGD2_4198 / Plasmid: pGEX-6p-2 / Details (production host): N-terminal GST tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9BS30, beta-lactamase
#2: Protein/peptide ALA-ALA-ARG-ASP-ALA-ALA-VAL-SER-ASP-ALA-ALA-ALA


Mass: 1089.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 1.95 Å3/Da / Density % sol: 36.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 250 microL reservoir (30% MPD, 12.5% polyethylene glycol 1500, 0.1 M Sodium Acetate buffer pH 4.5) with a 4 microL hanging drop (7.5 mg/ml protein, 15% MPD, 6.3% PEG 1500, 0.05 M sodium ...Details: 250 microL reservoir (30% MPD, 12.5% polyethylene glycol 1500, 0.1 M Sodium Acetate buffer pH 4.5) with a 4 microL hanging drop (7.5 mg/ml protein, 15% MPD, 6.3% PEG 1500, 0.05 M sodium acetate buffer pH 4.5), Loop-mounted crystals were flash-cooled without additional cryoprotectant and kept at 100 K with a nitrogen gas stream.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→38.1 Å / Num. obs: 76919 / % possible obs: 99.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 10.36 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 32
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 5 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 3884 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W4Q

3w4q


Resolution: 1.2→38.1 Å / SU ML: 0.0855 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 12.3556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.144 3845 5 %
Rwork0.1252 73050 -
obs0.1261 76895 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.24 Å2
Refinement stepCycle: LAST / Resolution: 1.2→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 52 264 2309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512117
X-RAY DIFFRACTIONf_angle_d0.91172898
X-RAY DIFFRACTIONf_chiral_restr0.0761345
X-RAY DIFFRACTIONf_plane_restr0.0053373
X-RAY DIFFRACTIONf_dihedral_angle_d15.6723759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.18741420.16072690X-RAY DIFFRACTION97.32
1.22-1.230.15841400.14372668X-RAY DIFFRACTION98.91
1.23-1.250.17761420.13322687X-RAY DIFFRACTION99.93
1.25-1.270.17821430.13922710X-RAY DIFFRACTION99.27
1.27-1.290.15191440.12862742X-RAY DIFFRACTION99.72
1.29-1.310.15411400.12192667X-RAY DIFFRACTION99.86
1.31-1.330.12041420.11342701X-RAY DIFFRACTION99.86
1.33-1.350.14021440.11422731X-RAY DIFFRACTION99.97
1.35-1.370.13631400.1152658X-RAY DIFFRACTION99.86
1.37-1.40.13611450.11132753X-RAY DIFFRACTION99.97
1.4-1.430.1341440.10712741X-RAY DIFFRACTION100
1.43-1.460.1621420.1122687X-RAY DIFFRACTION99.93
1.46-1.490.13381420.11152702X-RAY DIFFRACTION99.93
1.5-1.530.12171420.10512694X-RAY DIFFRACTION99.93
1.53-1.570.14281440.0992733X-RAY DIFFRACTION100
1.57-1.620.11851420.10072693X-RAY DIFFRACTION100
1.62-1.670.12921420.10622713X-RAY DIFFRACTION100
1.67-1.730.14961430.1132716X-RAY DIFFRACTION100
1.73-1.80.13981440.11992727X-RAY DIFFRACTION100
1.8-1.880.15271430.12132710X-RAY DIFFRACTION99.96
1.88-1.980.13011420.1212704X-RAY DIFFRACTION99.65
1.98-2.110.13251410.12482684X-RAY DIFFRACTION99.93
2.11-2.270.151420.12362693X-RAY DIFFRACTION99.61
2.27-2.50.14311420.13452702X-RAY DIFFRACTION100
2.5-2.860.14111440.14062734X-RAY DIFFRACTION99.93
2.86-3.60.15791420.13362707X-RAY DIFFRACTION100
3.6-38.10.14421420.1352703X-RAY DIFFRACTION99.93

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