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- PDB-9ltk: Crystal structur of Lpg1618(R215F) from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 9ltk
TitleCrystal structur of Lpg1618(R215F) from Legionella pneumophila
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-Lactamase / OXA-29
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiu, T. / Gao, J. / Ge, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370196 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Structural and molecular characterization of AmpS, a class D beta-lactamase from Legionella pneumophila.
Authors: Gao, J. / Liu, T. / Lu, L. / Zhou, Z. / Sun, W. / Chen, Y. / Xu, W. / Wang, N. / Ma, J. / Ge, H.
History
DepositionFeb 6, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,00322
Polymers59,0892
Non-polymers1,91320
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The enzyme exists in a monomeric form in solution as determined by size-exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.189, 156.189, 156.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-693-

HOH

21B-538-

HOH

31B-562-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 29544.635 Da / Num. of mol.: 2 / Mutation: R215F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Gene: lpg1618 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZV24, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O
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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.1M Tris-HCl pH7.2, 2.5M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 51671 / % possible obs: 100 % / Redundancy: 72.1 % / CC1/2: 0.998 / Net I/σ(I): 25
Reflection shellResolution: 1.9→1.95 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3747 / CC1/2: 0.723

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
autoPXdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18682 2502 4.9 %RANDOM
Rwork0.16972 ---
obs0.17056 48972 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.067 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3970 0 102 538 4610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124186
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163854
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.6545672
X-RAY DIFFRACTIONr_angle_other_deg0.7531.598889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5455492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg0.87516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48910731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024845
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021003
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1822.2191947
X-RAY DIFFRACTIONr_mcbond_other3.1822.2191947
X-RAY DIFFRACTIONr_mcangle_it4.0623.952431
X-RAY DIFFRACTIONr_mcangle_other4.0633.952432
X-RAY DIFFRACTIONr_scbond_it4.5242.7932239
X-RAY DIFFRACTIONr_scbond_other4.5232.7942240
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5834.8983237
X-RAY DIFFRACTIONr_long_range_B_refined8.97225.354998
X-RAY DIFFRACTIONr_long_range_B_other8.97225.354999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 169 -
Rwork0.265 3561 -
obs--100 %

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