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- PDB-7s0v: The role of an Asp-Asp pair in the structure, function and inhibi... -

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Basic information

Entry
Database: PDB / ID: 7s0v
TitleThe role of an Asp-Asp pair in the structure, function and inhibition of CTX-M Class A Beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE inhibitor / Inhibitor / Complex / Asp-Asp / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-J1X / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsKemp, M.T. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI161762 United States
CitationJournal: Febs Lett. / Year: 2021
Title: Mutation of the conserved Asp-Asp pair impairs the structure, function, and inhibition of CTX-M Class A beta-lactamase.
Authors: Kemp, M.T. / Nichols, D.A. / Zhang, X. / Defrees, K. / Na, I. / Renslo, A.R. / Chen, Y.
History
DepositionAug 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3992
Polymers28,0001
Non-polymers3991
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.620, 41.620, 231.162
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-577-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 27999.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9L5C7, beta-lactamase
#2: Chemical ChemComp-J1X / 3-(1H-pyrazol-1-yl)-N-[3-(1H-tetrazol-5-yl)phenyl]-5-(trifluoromethyl)benzamide


Mass: 399.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H12F3N7O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 1M KP1 pH 7.9 / PH range: 7.0-8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→38.53 Å / Num. obs: 17809 / % possible obs: 98.8 % / Redundancy: 6.6 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.058 / Rsym value: 0.054 / Net I/av σ(I): 7.6 / Net I/σ(I): 23.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-2.066.90.079.21765425480.0270.0760.0717.299.3
2.06-2.186.70.0679.11612124080.0270.0730.06718.998.9
2.18-2.336.40.0778.41446922460.0320.0840.07720.398.4
2.33-2.526.30.0579.91317020800.0230.0620.05721.798.3
2.52-2.766.10.05610.31214519950.0230.0610.05622.998.7
2.76-3.0860.0599.61056317530.0250.0640.05925.198.7
3.08-3.566.20.05410.7985516000.0220.0580.0542998.4
3.56-4.366.60.04810.7890113560.020.0520.04832.298.5
4.36-6.177.70.03713.7869411300.0140.040.03733.999.6
6.17-38.5278.30.0576.357516930.0230.0620.05734.499.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→38.527 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 1778 10.03 %
Rwork0.1889 15956 -
obs0.196 17734 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.1 Å2 / Biso mean: 21.1873 Å2 / Biso min: 3.24 Å2
Refinement stepCycle: final / Resolution: 1.95→38.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 29 221 2206
Biso mean--12.87 23.51 -
Num. residues----262
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-20.30681370.22031241137899
2-2.060.30781330.2191162129599
2.06-2.130.28521330.22131208134199
2.13-2.20.30911340.21211205133998
2.2-2.290.30151330.20991192132598
2.29-2.40.3141310.22231196132798
2.4-2.520.27691360.19671178131498
2.52-2.680.27541350.20521228136398
2.68-2.890.30771400.19641226136698
2.89-3.180.26221350.18681222135798
3.18-3.640.21451340.17361232136698
3.64-4.580.20641430.14391289143298
4.59-38.530.21111540.173813771531100

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