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- PDB-9mtv: Crystal structure of an apo-ADC-1 triple mutant -

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Basic information

Entry
Database: PDB / ID: 9mtv
TitleCrystal structure of an apo-ADC-1 triple mutant
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
NITRATE ION / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 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)81,3795
Polymers81,1932
Non-polymers1863
Water5,495305
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)40,5961
Polymers40,5961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7824
Polymers40,5961
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.089, 182.210, 50.767
Angle α, β, γ (deg.)90.00, 99.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 40596.277 Da / Num. of mol.: 2 / Mutation: V294F, S317T, F321S
Source method: isolated from a genetically manipulated source
Details: triple mutant 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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.27 Å3/Da / Density % sol: 45.87 %
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: 1.8→38.64 Å / Num. obs: 70428 / % possible obs: 98.7 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rpim(I) all: 0.045 / Rrim(I) all: 0.12 / Net I/σ(I): 9.2
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3910 / CC1/2: 0.676 / Rpim(I) all: 0.516

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→38.64 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2149 3399 4.84 %
Rwork0.1872 --
obs0.1885 70294 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→38.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5664 0 12 305 5981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075845
X-RAY DIFFRACTIONf_angle_d0.8267922
X-RAY DIFFRACTIONf_dihedral_angle_d17.4072222
X-RAY DIFFRACTIONf_chiral_restr0.053863
X-RAY DIFFRACTIONf_plane_restr0.0071027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.34231160.34292552X-RAY DIFFRACTION91
1.82-1.850.35411430.32172824X-RAY DIFFRACTION99
1.85-1.880.31181340.29872842X-RAY DIFFRACTION99
1.88-1.910.35171460.26792760X-RAY DIFFRACTION99
1.91-1.940.26051640.24812788X-RAY DIFFRACTION99
1.94-1.980.2541350.22172792X-RAY DIFFRACTION99
1.98-2.020.24611240.20952814X-RAY DIFFRACTION99
2.02-2.060.28491410.21642782X-RAY DIFFRACTION98
2.06-2.10.28171370.22792748X-RAY DIFFRACTION97
2.1-2.150.28651320.22372683X-RAY DIFFRACTION95
2.15-2.210.24471230.21812817X-RAY DIFFRACTION99
2.21-2.270.22151600.18752793X-RAY DIFFRACTION99
2.27-2.330.21371460.18992784X-RAY DIFFRACTION100
2.33-2.410.21751790.18822811X-RAY DIFFRACTION100
2.41-2.490.22931430.1822774X-RAY DIFFRACTION99
2.49-2.590.21051520.1942799X-RAY DIFFRACTION99
2.59-2.710.24671370.20032796X-RAY DIFFRACTION98
2.71-2.850.2681470.19932782X-RAY DIFFRACTION98
2.85-3.030.22731420.19092819X-RAY DIFFRACTION100
3.03-3.270.22781600.18982816X-RAY DIFFRACTION100
3.27-3.60.19521430.18442852X-RAY DIFFRACTION99
3.6-4.110.17311350.15692754X-RAY DIFFRACTION98
4.12-5.180.14151240.1362873X-RAY DIFFRACTION100
5.18-38.640.15071360.15482840X-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)
11.4204-0.93240.63711.88950.13391.0688-0.0877-0.07440.18940.2483-0.03930.0981-0.2574-0.1942-0.00030.2930.01870.00830.22750.00670.287613.3037-8.303811.847
21.3786-0.1506-0.35640.93840.13330.86450.06260.10190.0634-0.1782-0.0067-0.0113-0.0781-0.05060.00050.19230.0083-0.01010.20930.01910.146623.7072-27.9107-8.1952
31.055-0.6783-0.13431.5974-0.05751.1201-0.0003-0.11470.1080.0808-0.0145-0.175-0.0270.0880.00040.1838-0.00660.00170.24030.01710.191122.1973-28.26036.9646
41.7147-0.98730.58041.75760.61041.13560.0306-0.03740.2160.1387-0.0431-0.1829-0.01250.22020.00010.27960.00360.00120.26420.01120.253620.9356-18.369213.045
50.4648-0.2469-0.32831.5045-0.07510.77920.0310.286-0.284-0.3791-0.0935-0.01570.2881-0.10570.00030.35030.0078-0.01340.2958-0.02330.36392.48839.1897-3.458
60.83380.1274-0.16862.96110.08820.20590.0764-0.185-0.0561.0131-0.12980.2310.0843-0.0056-0.01010.4365-0.05130.03480.2420.01470.1927-3.274425.793219.1968
70.2478-0.4348-0.07962.77790.54690.3320.03210.06270.072-0.2298-0.11160.3107-0.04890.00990.00030.25760.0058-0.04350.27090.00510.2948-7.334532.05662.6359
80.8496-0.0998-0.69222.54490.26320.77370.06190.12980.0042-0.1674-0.1056-0.1115-0.07950.0180.00020.21650.0013-0.01520.23540.01750.22631.163120.78410.5746
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 309 )
4X-RAY DIFFRACTION4chain 'A' and (resid 310 through 361 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 46 )
6X-RAY DIFFRACTION6chain 'B' and (resid 47 through 241 )
7X-RAY DIFFRACTION7chain 'B' and (resid 242 through 309 )
8X-RAY DIFFRACTION8chain 'B' and (resid 310 through 359 )

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