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- PDB-6v1o: Structure of OXA-48 bound to QPX7728 at 1.80 A -

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Basic information

Entry
Database: PDB / ID: 6v1o
TitleStructure of OXA-48 bound to QPX7728 at 1.80 A
ComponentsOXA family beta-lactamase
KeywordsHYDROLASE/HYDROLASE Inhibitor / carbapenemase / boronate / inhibitor / beta-lactamase / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
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-RM9 / Beta-lactamase / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsPemberton, O.A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)HHSO100201600026C United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Cyclic Boronic Acid QPX7728, an Ultrabroad-Spectrum Inhibitor of Serine and Metallo-beta-lactamases.
Authors: Hecker, S.J. / Reddy, K.R. / Lomovskaya, O. / Griffith, D.C. / Rubio-Aparicio, D. / Nelson, K. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Parkinson, J. / Totrov, M. / Boyer, S.H. ...Authors: Hecker, S.J. / Reddy, K.R. / Lomovskaya, O. / Griffith, D.C. / Rubio-Aparicio, D. / Nelson, K. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Parkinson, J. / Totrov, M. / Boyer, S.H. / Glinka, T.W. / Pemberton, O.A. / Chen, Y. / Dudley, M.N.
History
DepositionNov 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Derived calculations
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OXA family beta-lactamase
B: OXA family beta-lactamase
C: OXA family beta-lactamase
D: OXA family beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,63318
Polymers123,4804
Non-polymers1,15314
Water26,3561463
1
A: OXA family beta-lactamase
B: OXA family beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3169
Polymers61,7402
Non-polymers5777
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-38 kcal/mol
Surface area19890 Å2
MethodPISA
2
C: OXA family beta-lactamase
D: OXA family beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3169
Polymers61,7402
Non-polymers5777
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-29 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.440, 105.550, 94.403
Angle α, β, γ (deg.)90.000, 107.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
OXA family beta-lactamase


Mass: 30869.881 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A482LRD5, UniProt: Q6XEC0*PLUS, beta-lactamase
#2: Chemical
ChemComp-RM9 / (1aR,7bS)-5-fluoro-2-hydroxy-1,1a,2,7b-tetrahydrocyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid


Mass: 221.978 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H8BFO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1463 / 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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride, 0.1 M Tris-HCl pH 8.5, 30% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→49.2 Å / Num. obs: 98181 / % possible obs: 97.6 % / Redundancy: 3.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.175 / Net I/σ(I): 7.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.96 / Num. measured all: 17432 / Num. unique obs: 4776 / CC1/2: 0.516 / Net I/σ(I) obs: 1.6 / % possible all: 95.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.81 Å38.85 Å
Translation3.81 Å38.85 Å

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHASER2.8.3phasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
iMOSFLM7.2.2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 1.8→38.85 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.59
RfactorNum. reflection% reflection
Rfree0.2238 3869 2.01 %
Rwork0.1583 --
obs0.1596 98160 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.5 Å2 / Biso mean: 17.4987 Å2 / Biso min: 3.22 Å2
Refinement stepCycle: final / Resolution: 1.8→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7953 0 74 1463 9490
Biso mean--14.01 31.87 -
Num. residues----972
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.820.32391350.27986271640689
1.82-1.850.37491280.27626491661994
1.85-1.870.32891320.26136491662394
1.87-1.890.28051390.24466686682595
1.89-1.920.34991340.2366556669095
1.92-1.950.30681360.23816708684495
1.95-1.980.26691360.21686574671096
1.98-2.010.30521390.2076766690596
2.01-2.050.26171370.20026651678896
2.05-2.090.26041410.19556660680196
2.09-2.130.2461310.18476635676696
2.13-2.170.22311440.16676765690996
2.17-2.220.2111290.16466715684497
2.22-2.270.26911400.16226714685497
2.27-2.320.24681390.16926781692097
2.32-2.390.21721400.16366708684897
2.39-2.460.22111560.15346865702197
2.46-2.540.24091350.14936754688998
2.54-2.630.17231400.1426871701198
2.63-2.730.22531410.14276743688498
2.73-2.860.23081350.13776856699198
2.86-3.010.19571380.14286834697298
3.01-3.20.18151380.13066837697598
3.2-3.440.17491450.11886878702399
3.44-3.790.16541410.11326870701198
3.79-4.340.20791400.11056831697199
4.34-5.460.18641390.11816924706399
5.46-38.850.17811410.14976774691598

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