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- PDB-9mtu: Crystal structure of apo-ADC-1 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 9mtu
TitleCrystal structure of apo-ADC-1 beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / class C / apo-enzyme
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
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,1892
Polymers81,1892
Non-polymers00
Water10,809600
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)40,5941
Polymers40,5941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)40,5941
Polymers40,5941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.144, 181.981, 50.334
Angle α, β, γ (deg.)90.00, 99.43, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.25 Å3/Da / Density % sol: 45.41 %
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: 0.95369 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.3→38.6 Å / Num. obs: 179263 / % possible obs: 96 % / Redundancy: 7 % / CC1/2: 0.999 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Net I/σ(I): 12.2
Reflection shellResolution: 1.3→1.32 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8242 / CC1/2: 0.718 / Rpim(I) all: 0.447

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→38.55 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 9081 5.07 %
Rwork0.152 --
obs0.1538 179059 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5589 0 0 600 6189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055812
X-RAY DIFFRACTIONf_angle_d0.7927892
X-RAY DIFFRACTIONf_dihedral_angle_d16.4222221
X-RAY DIFFRACTIONf_chiral_restr0.078866
X-RAY DIFFRACTIONf_plane_restr0.0061021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.30642490.27595064X-RAY DIFFRACTION86
1.31-1.330.27412880.22495472X-RAY DIFFRACTION93
1.33-1.350.26022900.20925648X-RAY DIFFRACTION95
1.35-1.360.23892960.20025611X-RAY DIFFRACTION95
1.36-1.380.26092860.20025637X-RAY DIFFRACTION95
1.38-1.40.2413370.18735658X-RAY DIFFRACTION96
1.4-1.420.20732980.18345569X-RAY DIFFRACTION96
1.42-1.440.26083110.18815722X-RAY DIFFRACTION96
1.44-1.460.23093290.17665570X-RAY DIFFRACTION96
1.46-1.490.22132860.15935738X-RAY DIFFRACTION95
1.49-1.510.20023080.15325593X-RAY DIFFRACTION96
1.51-1.540.19672840.14085262X-RAY DIFFRACTION88
1.54-1.570.18822650.13025720X-RAY DIFFRACTION97
1.57-1.60.18633290.12765630X-RAY DIFFRACTION96
1.6-1.640.18152780.13015735X-RAY DIFFRACTION97
1.64-1.680.16843010.12815671X-RAY DIFFRACTION96
1.68-1.720.16862640.13445671X-RAY DIFFRACTION96
1.72-1.760.18642960.14775794X-RAY DIFFRACTION98
1.76-1.820.20283010.15975722X-RAY DIFFRACTION97
1.82-1.870.1963020.15055732X-RAY DIFFRACTION96
1.87-1.940.19513120.1455454X-RAY DIFFRACTION93
1.94-2.020.183060.14155819X-RAY DIFFRACTION98
2.02-2.110.17963020.14675797X-RAY DIFFRACTION98
2.11-2.220.18213210.14425810X-RAY DIFFRACTION99
2.22-2.360.17433450.1445809X-RAY DIFFRACTION99
2.36-2.540.18582990.15155867X-RAY DIFFRACTION98
2.54-2.80.20453290.16185599X-RAY DIFFRACTION96
2.8-3.20.18253250.16365886X-RAY DIFFRACTION99
3.21-4.040.18463450.15175843X-RAY DIFFRACTION99
4.04-38.550.15282990.13495875X-RAY DIFFRACTION98

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