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- PDB-24tn: Crystal structure of class C beta-lactamase PDC-16 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 24tn
TitleCrystal structure of class C beta-lactamase PDC-16 in complex with imipenem
ComponentsBeta-lactamase
KeywordsHYDROLASE / Betalactamase / Antibiotic resistance
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
: / : / Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-IM2 / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiji, S.S. / Dhanasingh, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Structural and functional characterization of PDC-16 beta-lactamase reveals a constrained active-site architecture associated with altered catalysis.
Authors: Selvanose, L. / Veeraraghavan, B. / Dhanasingh, I.
History
DepositionMar 19, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,4945
Polymers78,7992
Non-polymers6953
Water5,783321
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7933
Polymers39,3991
Non-polymers3932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7012
Polymers39,3991
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.82, 90.02, 103.11
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase


Mass: 39399.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaPDC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Z1VQP5, beta-lactamase
#2: Chemical ChemComp-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N3O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.16 Å3/Da / Density meas: 43.25 Mg/m3 / Density % sol: 42.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350,100mM HEPES pH-7.5,225mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 16, 2025 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.2→51.61 Å / Num. obs: 35116 / % possible obs: 99.91 % / Redundancy: 9.6 % / CC1/2: 0.998 / Net I/σ(I): 5.94
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.099 / Num. unique obs: 2979 / Rrim(I) all: 0.11

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
iMOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S1S

6s1s


Resolution: 2.2→51.608 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.124 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.232
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 1788 5.099 %RANDOM
Rwork0.186 33278 --
all0.189 ---
obs-35066 99.909 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.825 Å2
Baniso -1Baniso -2Baniso -3
1--2.413 Å20 Å2-0 Å2
2--4.697 Å20 Å2
3----2.284 Å2
Refinement stepCycle: LAST / Resolution: 2.2→51.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5564 0 46 321 5931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125761
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165427
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.8217827
X-RAY DIFFRACTIONr_angle_other_deg0.5751.74912468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.325718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.53556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32410898
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.66210264
X-RAY DIFFRACTIONr_chiral_restr0.0760.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021374
X-RAY DIFFRACTIONr_nbd_refined0.2260.21343
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.25133
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22779
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.23031
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2375
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0620.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1520.219
X-RAY DIFFRACTIONr_nbd_other0.2580.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2970.27
X-RAY DIFFRACTIONr_mcbond_it3.1713.0622875
X-RAY DIFFRACTIONr_mcbond_other3.1713.0622875
X-RAY DIFFRACTIONr_mcangle_it4.7495.4933592
X-RAY DIFFRACTIONr_mcangle_other4.7495.4943593
X-RAY DIFFRACTIONr_scbond_it3.6513.4992886
X-RAY DIFFRACTIONr_scbond_other3.653.52887
X-RAY DIFFRACTIONr_scangle_it5.6796.2474235
X-RAY DIFFRACTIONr_scangle_other5.6786.2494236
X-RAY DIFFRACTIONr_lrange_it8.07431.6466666
X-RAY DIFFRACTIONr_lrange_other8.03231.4026595
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.2-2.2570.3131380.25424110.25725530.920.94699.84330.236
2.257-2.3190.2911240.23823580.24124820.9290.9531000.222
2.319-2.3860.2781340.21622950.2224290.9390.9621000.2
2.386-2.4590.2761300.20222170.20623500.9420.96699.87230.185
2.459-2.540.2621170.20221530.20522730.9430.96799.8680.185
2.54-2.6280.2661100.19421320.19822430.950.97199.95540.178
2.628-2.7270.297930.19620180.221170.9450.97299.71660.18
2.727-2.8380.3161050.19619350.20120410.9390.97499.9510.183
2.838-2.9640.258960.18818930.19219890.9560.9761000.175
2.964-3.1080.2851030.17718200.18219230.9360.9771000.167
3.108-3.2760.213980.16816960.1717940.9660.9811000.161
3.276-3.4740.259740.18216510.18517270.9570.97999.88420.179
3.474-3.7120.256890.18515240.18816150.9620.9899.87620.187
3.712-4.0080.204850.16914200.17115060.970.98299.93360.173
4.008-4.3880.205740.14813220.15113970.9710.98699.92840.156
4.388-4.9020.168590.14912270.1512890.9840.98799.76730.163
4.902-5.6510.209570.15910760.16211340.980.98799.91180.172
5.651-6.9010.243410.1849380.1869790.9790.9821000.195
6.901-9.6730.184400.1677380.1687780.9840.9811000.186
9.673-51.6080.283210.2474540.2484760.9230.9699.78990.291

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