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- PDB-7k5v: OXA-48 bound by Compound 3.1 -

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Basic information

Entry
Database: PDB / ID: 7k5v
TitleOXA-48 bound by Compound 3.1
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / beta-lactamase / carbapenemase / beta-lactamase inhibitor / complex / oxacillinase / 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
NAPHTHALENE-2,6-DISULFONIC ACID / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTaylor, D.M. / Hu, L. / Prasad, B.V.V. / 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: Acs Infect Dis. / Year: 2021
Title: Unique Diacidic Fragments Inhibit the OXA-48 Carbapenemase and Enhance the Killing of Escherichia coli Producing OXA-48.
Authors: Taylor, D.M. / Anglin, J. / Hu, L. / Wang, L. / Sankaran, B. / Wang, J. / Matzuk, M.M. / Prasad, B.V.V. / Palzkill, T.
History
DepositionSep 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 22, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 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: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,35610
Polymers56,5902
Non-polymers7668
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-58 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.922, 122.922, 161.143
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Beta-lactamase / Oxacillinase-48 / OXA-48


Mass: 28295.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_1, bla_2, bla_5, blaOXA-48, B6R99_29845, GJD56_28020, GJJ04_29145, KPE71T_00045, SAMEA3538918_02768, SAMEA3538961_03054, SAMEA3673128_05462
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical ChemComp-BIH / NAPHTHALENE-2,6-DISULFONIC ACID / 2,6-NAPHTHALENEDISULFONIC ACID / 2,6-NAPHTHALENEDISULPHONIC ACID


Mass: 288.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
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: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M TRIS 8.5 pH, 25 %v/v PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999957 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999957 Å / Relative weight: 1
ReflectionResolution: 2.8→29.61 Å / Num. obs: 18259 / % possible obs: 99.65 % / Redundancy: 16 % / Biso Wilson estimate: 47.53 Å2 / CC1/2: 0.961 / Rmerge(I) obs: 0.138 / Net I/σ(I): 24.4
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 5.17 / Num. unique obs: 1751

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3hbr

3hbr


Resolution: 2.8→29.61 Å / SU ML: 0.3231 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2367 960 5.26 %
Rwork0.1923 17297 -
obs0.1946 18257 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.75 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 45 0 4009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00284103
X-RAY DIFFRACTIONf_angle_d0.58625558
X-RAY DIFFRACTIONf_chiral_restr0.0456578
X-RAY DIFFRACTIONf_plane_restr0.0025738
X-RAY DIFFRACTIONf_dihedral_angle_d26.9952557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.950.32451260.27022382X-RAY DIFFRACTION98.51
2.95-3.130.33741450.27932410X-RAY DIFFRACTION100
3.13-3.370.30791290.2452428X-RAY DIFFRACTION100
3.37-3.710.25351530.21232432X-RAY DIFFRACTION100
3.71-4.250.20521330.17432477X-RAY DIFFRACTION100
4.25-5.350.20461380.15292504X-RAY DIFFRACTION99.92
5.35-29.610.17821360.15432664X-RAY DIFFRACTION100
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)
11.02431630838-0.389750343051.450154989984.110138403370.5458071001882.71277512968-0.2371430450240.196700044045-0.113102934233-0.2243289157020.09034595041490.53455358889-0.83932411240.1464812018190.2273707522360.698638053642-0.0701366852587-0.1390725177430.375349308752-0.05590526860730.81445767763550.43803041326.61019304824-21.8781217478
23.621815193611.332158580730.04291999567884.669284126930.2761701220162.40569050931-0.493378434160.3039121853460.539718076263-0.006826374518780.2658002437650.165909221774-0.1242740524290.08819931043450.03513752202970.529711249404-0.113425882339-0.1079924716110.2781966331440.03885989438240.51922577730153.92393208790.942565407997-26.7027457304
31.71486593481.2945777210.2281236025612.65549264037-0.1830669019772.65598244763-0.102118164236-0.0195856923672-0.1520202744620.1053997675910.172126468862-0.09379990285420.404813786197-0.15825862866-0.02453956542780.3739636528890.001436930108090.005547322622980.285976092282-0.02780145812410.35312137250756.6570262384-20.5176585811-12.4445475568
45.39171545914-0.0385549200444-2.578567260424.3059116702-0.3870831555427.72850596425-0.0692313001324-0.198151475915-0.6315620224020.0138007422607-0.0218573461769-0.5306319518610.8084099752550.8367849279520.1301492075670.3808586246460.0114717463421-0.02659318740280.259028804225-0.05460255080660.33199714277867.969727309-21.9699191647-14.3210964251
51.655515906120.4592897433851.445056807632.61212168751.203841483771.72710217043-0.166011943180.1270451959240.103542249539-0.1599184327520.130416593037-0.2492709808310.09887240454250.3633637860530.05925965770.358416716164-0.06441401919540.0587562953270.269994674515-0.05639166467060.34015237349465.7574661765-11.1447967692-17.8050551772
61.10216629864-0.008459198833041.205329130891.423526821440.6229975557861.882157744970.04283054197690.1374848439360.00626616190985-0.005494209616750.129042760708-0.0458826972677-0.06152669380820.0920541640822-0.1927858723460.395796841985-0.08647448288060.06816542926690.290044471316-0.006241573056910.34315355938254.5605357639-15.7052114446-21.8883006699
71.629380028890.5359052711340.784090707063.280698229670.3126418544453.65692964896-0.2935278587460.03396889871490.195117280158-0.2039698183680.05956793719240.281087625902-0.311289044378-0.3736860450180.2242621591990.334340346329-0.0316800399979-0.01359706768540.249664838744-0.02796637842790.38990422665248.3150866677-4.74542483659-20.8858654362
83.228991806970.5762503318620.7074173728321.66061430882-0.1827431816253.475008048310.187908437208-0.4887220007150.4316891214810.5410891942570.220064826630.4446622429160.169820956533-1.16035436182-0.2409908402180.57822085008-0.4223372664090.2771903080380.761369042009-0.2102989955390.79916144630321.5077307318-35.7851080952-22.2949120024
93.252105396060.1261218890160.3491962561242.97792405233-0.09523966504681.49149491523-0.2117786800670.0417688800349-0.3507884648650.6629289100150.01550088113920.142653766670.0451747900604-0.06774356944170.09233715978110.630176237777-0.226658643970.08067130741970.4485371881-0.03764761169150.45657319253229.394923954-37.7189586176-22.5892504742
101.55282004845-0.0708220106032-0.2538258922951.54034601872-0.2535368582141.33929473854-0.05405544044280.2681423778990.0456291322757-0.1415833754740.029165703951-0.02118051229290.0434383373433-0.03062567116270.03655663072410.428237572165-0.117014810447-0.0158041691150.362548541199-0.02181634355710.3491515817240.5164443612-29.1369186401-44.4524143399
113.087322478460.5140724827270.8901048546222.289019870510.7476058421362.499169987240.21223885514-0.0358100303697-0.3827639478850.1441390543720.138005576749-0.005934953606150.191848529760.192208127233-0.3057724407820.341868637609-0.0950542066503-0.002293291406210.338031164849-0.04635971556190.32343269250142.7091630253-35.664131935-34.9479303521
122.330462050751.111452483430.7500760415452.539594211872.439724810053.45073055151-0.0435672961395-0.3139252057070.08128383823510.204199134435-0.1990231063240.3826506580610.0371055998817-0.4565528807680.1869764030960.383189000627-0.09229613403060.05475498724070.321194496438-0.005898790291790.33594943377534.3872526256-27.6266162605-29.995630435
134.85927834003-1.170692914033.106541655292.165899868280.06689062597155.53058958853-0.0537334766526-0.5527707534460.6986088899660.27929524809-0.2315917759040.36736768087-0.0907059459625-0.8659865901450.2698175867480.366354098379-0.1286500994560.1203706760220.381197372251-0.09080877043530.52510549203927.1361191823-27.894955533-26.2267224119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 142 )
5X-RAY DIFFRACTION5chain 'A' and (resid 143 through 177 )
6X-RAY DIFFRACTION6chain 'A' and (resid 178 through 218 )
7X-RAY DIFFRACTION7chain 'A' and (resid 219 through 265 )
8X-RAY DIFFRACTION8chain 'B' and (resid 24 through 38 )
9X-RAY DIFFRACTION9chain 'B' and (resid 39 through 58 )
10X-RAY DIFFRACTION10chain 'B' and (resid 59 through 155 )
11X-RAY DIFFRACTION11chain 'B' and (resid 156 through 194 )
12X-RAY DIFFRACTION12chain 'B' and (resid 195 through 231 )
13X-RAY DIFFRACTION13chain 'B' and (resid 232 through 265 )

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