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- PDB-8dod: Beta-lactamase CTX-M-14 S130A -

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Basic information

Entry
Database: PDB / ID: 8dod
TitleBeta-lactamase CTX-M-14 S130A
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / CTX-M-14 / mutation / B-lactam / antibiotic resistance
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsLu, S. / Palzkill, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Mutagenesis and structural analysis reveal the CTX-M beta-lactamase active site is optimized for cephalosporin catalysis and drug resistance.
Authors: Lu, S. / Montoya, M. / Hu, L. / Neetu, N. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.
History
DepositionJul 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0072
Polymers27,9681
Non-polymers391
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.490, 41.490, 230.780
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-lactamase


Mass: 27967.516 Da / Num. of mol.: 1 / Mutation: S130A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: H6UQI0, beta-lactamase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl pH 8.5, 25% (W/V) PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.61→35.504 Å / Num. obs: 62179 / % possible obs: 99.46 % / Redundancy: 2 % / Biso Wilson estimate: 17.44 Å2 / Rmerge(I) obs: 0.0143 / Rrim(I) all: 0.02023 / Net I/σ(I): 20.94
Reflection shellResolution: 1.61→1.668 Å / Rmerge(I) obs: 0.0634 / Num. unique obs: 6092 / Rrim(I) all: 0.09381 / % possible all: 99.25

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.61→35.504 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 2004 6.45 %
Rwork0.2218 29080 -
obs0.2242 31084 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.76 Å2 / Biso mean: 33.0089 Å2 / Biso min: 10.34 Å2
Refinement stepCycle: final / Resolution: 1.61→35.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 0 207 2170
Biso mean---33.78 -
Num. residues----263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6101-1.65030.391400.3017202999
1.6503-1.69490.32681380.2811198799
1.6949-1.74480.37051400.2798206799
1.7448-1.80110.32471440.2605206799
1.8011-1.86550.29721390.2651199199
1.8655-1.94020.28131440.25532061100
1.9402-2.02850.31061440.25522029100
2.0285-2.13540.28851350.24742079100
2.1354-2.26920.25981410.23572069100
2.2692-2.44440.27241450.2322109100
2.4444-2.69030.25881380.21852070100
2.6903-3.07940.23181480.21022118100
3.0794-3.87890.22541480.1932214399
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)
10.84350.1437-0.2160.1562-0.20121.54890.10440.0985-0.2042-0.10130.04220.00330.7877-0.0125-0.12420.7160.1467-0.15220.2757-0.01960.17393.5389-16.3927-31.2385
21.6763-0.4879-0.63731.4688-0.4192.51710.1697-0.0186-0.2892-0.1195-0.0740.09990.8069-0.47650.02760.2586-0.0796-0.09650.24690.02750.1911-5.1541-9.9726-16.3963
33.24141.3919-0.96121.8138-0.52290.89620.1062-0.27680.19060.2103-0.05060.291-0.1434-0.4072-0.08450.22340.05320.07860.54920.02540.2792-12.151311.0298-4.9073
40.7097-0.1127-0.090.57260.03370.34140.0189-0.06850.2366-0.00950.0164-0.0496-0.2826-0.2457-0.0350.24590.16870.04810.28530.06340.2277-7.02712.5342-14.6342
50.7538-0.2195-0.02281.08020.33011.89150.13490.06770.0833-0.00990.106-0.12440.2945-0.0632-0.17120.1094-0.003-0.02660.14610.02070.15110.8541-2.399-9.2969
62.0389-0.18040.02610.66950.07490.1733-0.04830.0544-0.21230.01250.0320.09920.3174-0.212-0.00450.4736-0.1961-0.05230.25320.03210.1811-6.0975-13.0818-16.7228
70.3702-0.2030.08220.1158-0.02870.07740.0326-0.0302-0.1080.0338-0.00810.1080.1098-0.2644-0.06360.2086-0.2666-0.07150.79510.06980.2238-18.0783-4.6798-15.6966
80.6236-0.4411-0.43091.1929-0.28760.6949-0.04690.15310.0044-0.10820.13570.20320.0535-0.5264-0.01760.1362-0.0231-0.02860.33330.04540.1584-9.139-2.8149-31.954
91.18730.0830.50020.5861-0.18090.95640.05530.2049-0.1105-0.07920.13540.03020.4186-0.0884-0.12130.1307-0.0457-0.0330.349-0.01030.1785-1.0765-5.5373-26.189
102.61610.20350.07882.61210.48042.52770.14580.2408-0.2328-0.19950.10020.12660.6424-0.3994-0.14250.3743-0.055-0.07120.22350.01050.1638-2.4548-10.4338-34.7005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 50 )A26 - 50
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 86 )A51 - 86
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 101 )A87 - 101
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 129 )A102 - 129
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 179 )A130 - 179
6X-RAY DIFFRACTION6chain 'A' and (resid 180 through 194 )A180 - 194
7X-RAY DIFFRACTION7chain 'A' and (resid 195 through 212 )A195 - 212
8X-RAY DIFFRACTION8chain 'A' and (resid 213 through 229 )A213 - 229
9X-RAY DIFFRACTION9chain 'A' and (resid 230 through 275 )A230 - 275
10X-RAY DIFFRACTION10chain 'A' and (resid 276 through 290 )A276 - 290

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