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- PDB-7dml: OXA-48 carbapenemase in complex with (R)-2-(1-hydroxy-1,3-dihydro... -

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Basic information

Entry
Database: PDB / ID: 7dml
TitleOXA-48 carbapenemase in complex with (R)-2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)acrylic acid
ComponentsBeta-lactamase
KeywordsHYDROLASE / carbapenemase / serine-beta-lactamase / ANTIBIOTIC
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-H9O / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.936 Å
AuthorsLi, G.-B. / Yan, Y.-H.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)81874291 China
National Science Foundation (NSF, China)82073698 China
CitationJournal: Chem.Commun.(Camb.) / Year: 2021
Title: Design and enantioselective synthesis of 3-(alpha-acrylic acid) benzoxaboroles to combat carbapenemase resistance
Authors: Xiao, Y.C. / Chen, X.P. / Deng, J. / Yan, Y.H. / Zhu, K.R. / Li, G. / Yu, J.L. / Brem, J. / Chen, F. / Schofield, C.J. / Li, G.B.
History
DepositionDec 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5758
Polymers121,7594
Non-polymers8164
Water17,655980
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6442
Polymers30,4401
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6442
Polymers30,4401
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6442
Polymers30,4401
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6442
Polymers30,4401
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.455, 105.865, 94.118
Angle α, β, γ (deg.)90.000, 107.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase


Mass: 30439.725 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, bla_2, bla_3, blaOXA-48 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical
ChemComp-H9O / 2-[(3R)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid


Mass: 203.987 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9BO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 980 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 5% 1-butanol, 11-17% (v/v) Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.936→19.81 Å / Num. obs: 79729 / % possible obs: 98.32 % / Redundancy: 6.7 % / Biso Wilson estimate: 17.15 Å2 / CC1/2: 0.999 / Net I/σ(I): 20.8
Reflection shellResolution: 1.94→2.01 Å / Num. unique obs: 79729 / CC1/2: 0.999

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.94 Å19.81 Å
Translation1.94 Å19.81 Å

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Processing

Software
NameVersionClassification
PHASER2.6.0phasing
PHENIX1.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P98

6p98


Resolution: 1.936→19.809 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 16.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.172 1999 2.57 %
Rwork0.138 75642 -
obs0.1389 77641 95.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.92 Å2 / Biso mean: 20.7849 Å2 / Biso min: 2.77 Å2
Refinement stepCycle: final / Resolution: 1.936→19.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7896 0 60 980 8936
Biso mean--25.76 28.98 -
Num. residues----964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018192
X-RAY DIFFRACTIONf_angle_d1.111097
X-RAY DIFFRACTIONf_chiral_restr0.111159
X-RAY DIFFRACTIONf_plane_restr0.0061429
X-RAY DIFFRACTIONf_dihedral_angle_d21.0924801
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.936-1.98430.23871250.1785458582
1.9843-2.03790.18911400.144552398
2.0379-2.09780.17621480.1387552198
2.0978-2.16540.2141470.1396555098
2.1654-2.24270.1851470.1394550598
2.2427-2.33240.20211450.1395549198
2.3324-2.43830.17631390.1379550298
2.4383-2.56660.1811470.135546697
2.5666-2.7270.1971460.1379546497
2.727-2.9370.16851470.1452547697
2.937-3.23140.1751420.1465540896
3.2314-3.69640.171490.1295541996
3.6964-4.64710.13621390.1225544395
4.6471-19.8090.14021380.1402528992

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