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- PDB-9mtw: Crystal structure of ADC-1-ertapenem complex -

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Basic information

Entry
Database: PDB / ID: 9mtw
TitleCrystal structure of ADC-1-ertapenem complex
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / ANTIBIOTIC / beta-lactamase / class C / ertapenem / acyl-enzyme complex / HYDROLASE / HYDROLASE-INHIBITOR / ANTIBIOTIC complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / 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-1RG / : / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsSmith, C.A. / Stewart, N.K. / Vakulenko, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI155723 United States
CitationJournal: Mbio / Year: 2025
Title: Evolution of carbapenemase activity in the class C beta-lactamase ADC-1.
Authors: Stewart, N.K. / Toth, M. / Bhattacharya, M. / Smith, C.A. / Vakulenko, S.B.
History
DepositionJan 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 18, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,2686
Polymers81,1892
Non-polymers1,0794
Water7,116395
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1343
Polymers40,5941
Non-polymers5402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1343
Polymers40,5941
Non-polymers5402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.994, 183.065, 50.451
Angle α, β, γ (deg.)90.00, 98.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 40594.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ADC-1 beta-lactamase / Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ampC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L4R5, beta-lactamase
#2: Chemical ChemComp-1RG / (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid / ERTAPENEM, bound form PRE-ISOMERIZED


Mass: 477.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N3O7S / Comment: medication, antibiotic*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A1B93 / (2S,3R,4R)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / ertapenem, bound form, post-isomerized, delta-1(R) isomer


Mass: 477.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N3O7S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M lithium chloride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→38.63 Å / Num. obs: 99666 / % possible obs: 98.6 % / Redundancy: 4 % / CC1/2: 0.997 / Rpim(I) all: 0.039 / Rrim(I) all: 0.08 / Net I/σ(I): 9.8
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4852 / CC1/2: 0.491 / Rpim(I) all: 0.577

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→38.63 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 4946 4.97 %
Rwork0.1825 --
obs0.1837 99491 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5573 0 74 395 6042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065835
X-RAY DIFFRACTIONf_angle_d0.9827914
X-RAY DIFFRACTIONf_dihedral_angle_d16.7612235
X-RAY DIFFRACTIONf_chiral_restr0.062868
X-RAY DIFFRACTIONf_plane_restr0.0071020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.28151520.27453024X-RAY DIFFRACTION94
1.62-1.640.27561620.24563156X-RAY DIFFRACTION99
1.64-1.660.23161600.23283214X-RAY DIFFRACTION99
1.66-1.680.23291610.22663136X-RAY DIFFRACTION99
1.68-1.70.24371730.22943155X-RAY DIFFRACTION99
1.7-1.720.23341720.22263156X-RAY DIFFRACTION98
1.72-1.750.2781510.22923124X-RAY DIFFRACTION98
1.75-1.770.28091720.24483113X-RAY DIFFRACTION97
1.77-1.80.27551910.25163097X-RAY DIFFRACTION97
1.8-1.830.24641880.23242907X-RAY DIFFRACTION94
1.83-1.860.24841730.21743241X-RAY DIFFRACTION100
1.86-1.90.2951800.23493096X-RAY DIFFRACTION99
1.9-1.930.24051600.19923208X-RAY DIFFRACTION99
1.93-1.970.22681690.19363155X-RAY DIFFRACTION99
1.97-2.020.21781460.18613217X-RAY DIFFRACTION99
2.02-2.060.21381690.19383153X-RAY DIFFRACTION99
2.06-2.110.22571390.19553153X-RAY DIFFRACTION98
2.11-2.170.2561530.19723097X-RAY DIFFRACTION97
2.17-2.240.20851670.1933097X-RAY DIFFRACTION97
2.24-2.310.22661440.19373224X-RAY DIFFRACTION99
2.31-2.390.21581730.18983196X-RAY DIFFRACTION99
2.39-2.490.19871660.18143149X-RAY DIFFRACTION100
2.49-2.60.21191470.18473198X-RAY DIFFRACTION99
2.6-2.740.23011710.19313182X-RAY DIFFRACTION99
2.74-2.910.2431730.19053118X-RAY DIFFRACTION98
2.91-3.130.21941870.18823188X-RAY DIFFRACTION100
3.13-3.450.20341640.18313197X-RAY DIFFRACTION99
3.45-3.940.17351700.16663191X-RAY DIFFRACTION99
3.95-4.970.141390.13393171X-RAY DIFFRACTION98
4.97-38.630.15991740.14453232X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8978-0.61150.44221.0757-0.00090.6808-0.0959-0.14380.18260.31320.00780.1786-0.3585-0.099-0.00650.260.03160.03290.19760.01390.222313.278-8.423511.6112
21.2963-0.1755-0.06410.7869-0.02380.9174-0.01070.06880.005-0.11410.03470.0389-0.0313-0.05170.00070.1289-0.001-0.01660.16210.01940.113223.5278-28.3548-8.1662
31.0339-0.14010.22140.9766-0.06361.20250.008-0.06170.02810.0749-0.0056-0.0188-0.07290.0016-0.00050.1339-0.00750.00640.18010.02310.128521.3284-24.97038.9669
40.5352-0.1695-0.1950.2268-0.13060.2870.25380.4005-0.5572-0.4904-0.1612-0.38530.45950.01370.0030.36380.0299-0.00980.2823-0.0260.41356.43799.677-5.1117
50.3479-0.1668-0.39940.94040.23990.5827-0.04860.017-0.29690.00890.01620.17710.1208-0.00610.00020.2330.0009-0.04870.18990.01260.35252.63817.97445.7822
60.0750.2008-0.09461.6739-0.1790.15030.1298-0.32280.01371.4387-0.20640.1925-0.0246-0.0119-0.07020.643-0.08710.12040.244-0.00880.2288-5.12536.364421.5875
70.6807-0.1562-0.34781.15850.38530.2852-0.1472-0.1878-0.24340.929-0.00410.31540.08950.0941-0.01090.4585-0.0220.0570.23250.04720.3108-5.333915.480217.4124
80.4976-0.9421-0.21462.10410.34420.51560.06680.03150.0081-0.1701-0.11530.2495-0.1012-0.1017-0.00360.18980.0108-0.00670.2074-0.00730.265-6.89432.20712.7631
90.8208-0.0466-0.6781.95140.31260.7570.08290.105-0.0464-0.2517-0.0853-0.11770.0065-0.017300.17440.0067-0.01340.18180.00950.23621.965320.80460.4391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 210 )
3X-RAY DIFFRACTION3chain 'A' and (resid 211 through 361 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 28 )
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 64 )
6X-RAY DIFFRACTION6chain 'B' and (resid 65 through 168 )
7X-RAY DIFFRACTION7chain 'B' and (resid 169 through 241 )
8X-RAY DIFFRACTION8chain 'B' and (resid 242 through 309 )
9X-RAY DIFFRACTION9chain 'B' and (resid 310 through 360 )

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