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- PDB-6xqr: OXA-48 bound by Compound 2.2 -

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Basic information

Entry
Database: PDB / ID: 6xqr
TitleOXA-48 bound by Compound 2.2
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / beta-lactamase / carbapenemase / beta-lactamase inhibitor / complex / oxacillinase / 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
[1,1'-biphenyl]-4,4'-disulfonic acid / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionJul 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2545
Polymers56,5902
Non-polymers6643
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-8 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.561, 122.561, 161.284
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
Details: Residues GHM precede the mature OXA-48 sequence; they were left behind after TEV protease cleavage
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-VBV / [1,1'-biphenyl]-4,4'-disulfonic acid


Mass: 314.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10O6S2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 3.13 Å3/Da / Density % sol: 60.67 %
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: 2.2→30 Å / Num. obs: 36903 / % possible obs: 100 % / Redundancy: 19 % / Biso Wilson estimate: 29.76 Å2 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.028 / Rrim(I) all: 0.125 / Net I/σ(I): 30.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 1808 / CC1/2: 0.963 / Rpim(I) all: 0.172 / Rrim(I) all: 0.769 / % possible all: 100

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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: 2.2→29.55 Å / SU ML: 0.187 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2037 1866 5.06 %
Rwork0.1678 34976 -
obs0.1696 36842 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 41 295 4300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314104
X-RAY DIFFRACTIONf_angle_d0.5715560
X-RAY DIFFRACTIONf_chiral_restr0.044582
X-RAY DIFFRACTIONf_plane_restr0.0027738
X-RAY DIFFRACTIONf_dihedral_angle_d27.0631560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.29341400.22712635X-RAY DIFFRACTION100
2.26-2.330.25661490.20592639X-RAY DIFFRACTION100
2.33-2.40.19241330.18582649X-RAY DIFFRACTION100
2.4-2.490.20851630.18372610X-RAY DIFFRACTION100
2.49-2.590.24011480.17812646X-RAY DIFFRACTION100
2.59-2.710.24581460.18612653X-RAY DIFFRACTION100
2.71-2.850.25671380.18542667X-RAY DIFFRACTION100
2.85-3.030.22631200.19772686X-RAY DIFFRACTION100
3.03-3.260.24061280.18732700X-RAY DIFFRACTION100
3.26-3.590.19871550.16392679X-RAY DIFFRACTION99.96
3.59-4.10.19171370.14942735X-RAY DIFFRACTION99.97
4.11-5.170.15661490.13762754X-RAY DIFFRACTION100
5.17-29.550.17211600.15072923X-RAY DIFFRACTION99.9
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)
11.43244058689-0.4366033656090.1797450660393.153713613710.7571912081792.61069930002-0.2056206983030.1871027848240.51558095542-0.2857211038350.2047388415130.445934375626-1.13585468936-0.0619375824309-0.03927090085360.824343725413-0.0285843316729-0.1516052369030.260063128663-0.008687464679080.67682883115550.3134846366.77643133263-22.0416096577
21.797590998860.7401170392810.7351555811873.0816699965-0.9199099425722.41885117765-0.3602500637420.1617287974730.32944595566-0.2540396118590.311280613496-0.0236685066247-0.4364676703520.1261262080940.09391787993370.414201726328-0.11533097501-0.02246678364470.183507290577-0.0182949688020.26990962596558.0674404721-5.25050926159-21.7624155474
33.149561128740.999192267111-0.3193493440494.179207755860.1542040994392.62649997518-0.150028970133-0.357856305082-0.2576627155010.4502169985340.0662020208307-0.07615238283110.6494550131190.0795537433557-0.04980723419420.482211428635-0.00369609145607-0.02321364910620.24433613688-0.02324720330590.25408520127355.6822602281-28.6220927931-9.18063549084
43.1105884230.960001384190.8358496900495.830456122810.9042528579983.49939778896-0.129323754736-0.377811141660.1501232374950.4934207084140.05792082393170.1524642473560.451582231236-0.316278813813-0.006761515940620.344535162595-0.06291994099210.04992754993750.208303489809-0.0411889403240.24742774509850.2695815011-23.4140541553-9.80835182704
56.351188004791.5319623032-4.424148631164.57027802023-3.108813212997.45085686994-0.381406281543-0.105662330612-0.446286286507-0.1275005495790.130214684218-0.5130158526370.568027060240.6878150661510.291652009630.3027149943690.0261810531892-0.01787454858430.22969979342-0.1276882468450.26574436219867.6916162274-21.7990560899-14.4215477821
61.580978266370.2389689191061.049427724771.915359254950.5853548008192.31478443598-0.196735870870.2700943127840.0182289190242-0.1392173259870.226503525144-0.189904082708-0.1698725802650.41968021428-0.03327366967050.269803452498-0.1074589609960.04292698219830.225011357539-0.04556629834870.23770094329463.4449130521-14.7335458141-21.5266749562
72.43416927340.8177337369541.076109427932.668866648460.02574780876691.32929678078-0.30441221710.02933598466820.257150264943-0.1423961760870.1069865306210.208610686154-0.426542869149-0.2395497352730.2337916636030.326210001238-0.045474083928-0.00446422740350.160638189253-0.02770636900580.25649112086550.9946176221-8.3749489464-19.5960472826
82.187430823450.827988125121-0.07052306858573.036215140480.6980701617925.54705774688-0.3092625561580.1638848088160.230918338281-0.2076972490780.004047933135040.630463856936-0.919955769479-0.8469938926070.3453434077460.3847060543890.0619028492764-0.1044411903150.226607293893-0.07075649195590.50247229983344.0013585541-2.32043056068-19.6804014909
94.486112298331.285494663960.69861252932.80138017065-0.576777489731.821150877710.208882643436-0.524077151747-0.05851205697860.571037038746-0.2454641329080.6172159889170.540958483988-0.920600801521-0.04695610448830.541086795116-0.349769252910.1839048997810.541999279164-0.1586035046840.48205066561825.5975333771-36.6336269292-22.5681309677
100.863978075607-0.3714610775230.4558584945841.56422182370.2607611936351.72550200099-0.02611067122450.1851692705170.143974534972-0.0347571061427-0.08621168526120.0538875407139-0.0971920816225-0.04135045595970.1147880531030.330206673097-0.1598939783470.001923399916340.266400033614-0.01779698230230.27980222147339.568313007-24.8008047285-42.7909598193
112.36044513802-1.811268150710.6717039980274.437905661260.6049351446072.43608284341-0.07243984032650.193163510194-0.0529340045787-0.2087282270860.1044964535070.05322959622730.07226461708780.332576816179-0.05422801655340.355556433523-0.2024024895850.02640146113040.283652134903-0.03277853661750.23692060491144.0739156136-33.721851797-48.5186843636
121.600646059040.5338476775040.3602482762181.95893706941.214081830122.57852559952-0.0927452205103-0.008549023821220.04867391110970.06929070216-0.07319519066280.3516807560750.168527335898-0.3890035371580.1580411131460.282035360066-0.152967450430.03663968130240.250789350601-0.02798122785550.28770190331835.2905714025-31.4016670575-32.3699549315
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 82 )
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 102 )
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 119 )
5X-RAY DIFFRACTION5chain 'A' and (resid 120 through 142 )
6X-RAY DIFFRACTION6chain 'A' and (resid 143 through 194 )
7X-RAY DIFFRACTION7chain 'A' and (resid 195 through 243 )
8X-RAY DIFFRACTION8chain 'A' and (resid 244 through 265 )
9X-RAY DIFFRACTION9chain 'B' and (resid 24 through 58 )
10X-RAY DIFFRACTION10chain 'B' and (resid 59 through 119 )
11X-RAY DIFFRACTION11chain 'B' and (resid 120 through 141 )
12X-RAY DIFFRACTION12chain 'B' and (resid 142 through 265 )

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