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- PDB-7ti0: Structure of CTX-M-15 bound to RPX-7063 at 1.5A -

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Basic information

Entry
Database: PDB / ID: 7ti0
TitleStructure of CTX-M-15 bound to RPX-7063 at 1.5A
ComponentsBeta-lactamase
KeywordsHYDROLASE / CTX-M-15 / ANTIBIOTIC
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ZXQ / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsClifton, M.C. / Abendroth, J. / Hecker, S.J. / Edwards, T.E.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Bioorg.Med.Chem. / Year: 2022
Title: Broad-spectrum cyclic boronate beta-lactamase inhibitors featuring an intramolecular prodrug for oral bioavailability.
Authors: Reddy, K.R. / Totrov, M. / Lomovskaya, O. / Griffith, D.C. / Tarazi, Z. / Clifton, M.C. / Hecker, S.J.
History
DepositionJan 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)28,7386
Polymers28,1391
Non-polymers5995
Water5,278293
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.880, 44.780, 117.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 28138.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: blaCTX-M-15, bla_1, bla_10, bla_2, bla_3, blaCTX-M, CTX-M, CTX-M-15, ctx-m-15
Production host: Escherichia coli (E. coli) / References: UniProt: Q2PUH3, beta-lactamase

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Non-polymers , 5 types, 298 molecules

#2: Chemical ChemComp-ZXQ / {(3R,7S)-2-hydroxy-3-[2-(thiophen-2-yl)acetamido]-2,3,4,7-tetrahydro-1,2-oxaborepin-7-yl}acetic acid


Mass: 309.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16BNO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M bis-tris propane pH 7.0, 2.3M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2011
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 39211 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.97 % / Biso Wilson estimate: 12.638 Å2 / Rmerge(I) obs: 0.06 / Net I/av σ(I): 18.79 / Net I/σ(I): 18.79
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
1.5-1.543.870.2296.12862199.3
1.54-1.5840.20172772199.6
1.58-1.634.010.17282734199.6
1.63-1.684.020.1499.22634199.5
1.68-1.7340.13110.22585199.6
1.73-1.794.040.109122481199.6
1.79-1.864.020.0914.22387199.5
1.86-1.9440.074172331199.8
1.94-2.024.020.063202222199.8
2.02-2.123.980.055222134199.6
2.12-2.2440.04924.22025199.6
2.24-2.373.970.04526.31935199.5
2.37-2.5440.043281792199
2.54-2.744.010.0428.71687198.5
2.74-33.940.03731.31555198.4
3-3.353.870.03433.61411198.2
3.35-3.873.80.0337.31241197.6
3.87-4.743.90.02738.81066197.5
4.74-6.713.840.02737.2864197.8
6.71-503.60.02738.4493195.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1yms

1yms


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.975 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 1965 5 %RANDOM
Rwork0.16 37246 --
obs0.16 39211 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.305 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1927 0 36 293 2256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192000
X-RAY DIFFRACTIONr_bond_other_d0.0010.021327
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.9832722
X-RAY DIFFRACTIONr_angle_other_deg1.5233253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8265263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94924.28677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.83815329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.1241515
X-RAY DIFFRACTIONr_chiral_restr0.340.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212237
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02378
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 126 -
Rwork0.185 2525 -
all-2651 -
obs--98.99 %
Refinement TLS params.Method: refined / Origin x: 45.4793 Å / Origin y: 38.8027 Å / Origin z: 12.2183 Å
111213212223313233
T0.0161 Å2-0.0033 Å20.0042 Å2-0.0051 Å2-0.0009 Å2--0.002 Å2
L0.8703 °2-0.037 °20.0225 °2-0.4021 °2-0.0251 °2--0.3679 °2
S0.0007 Å °-0.0355 Å °0.0206 Å °-0.008 Å °-0.0039 Å °-0.0137 Å °0.0025 Å °0.0103 Å °0.0033 Å °

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