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- PDB-7r6z: OXA-48 bound by Compound 3.3 -

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Basic information

Entry
Database: PDB / ID: 7r6z
TitleOXA-48 bound by Compound 3.3
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 / metal ion binding
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
4-amino-5-hydroxynaphthalene-2,7-disulfonic acid / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTaylor, D.M. / Hu, L. / Prasad, B.V.V. / Sankaran, B. / 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
DepositionJun 24, 2021Deposition 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)57,70412
Polymers56,5902
Non-polymers1,11410
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.808, 121.808, 160.462
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
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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: GHM residues are left behind at N-terminus after TEV 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

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Non-polymers , 5 types, 309 molecules

#2: Chemical ChemComp-3I0 / 4-amino-5-hydroxynaphthalene-2,7-disulfonic acid


Mass: 319.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9NO7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris HCl pH 8.5, 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: 8.2.1 / Wavelength: 0.999889 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999889 Å / Relative weight: 1
ReflectionResolution: 2.1→34.35 Å / Num. obs: 41784 / % possible obs: 99.92 % / Redundancy: 26.1 % / Biso Wilson estimate: 23.91 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 34.125
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 26.4 % / Rmerge(I) obs: 0.803 / Num. unique obs: 4062 / Rrim(I) all: 0.819

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2.1→34.35 Å / SU ML: 0.1752 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.3654
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1951 2044 4.9 %
Rwork0.166 39663 -
obs0.1675 41707 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 66 299 4329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214122
X-RAY DIFFRACTIONf_angle_d0.47265578
X-RAY DIFFRACTIONf_chiral_restr0.0409582
X-RAY DIFFRACTIONf_plane_restr0.0029742
X-RAY DIFFRACTIONf_dihedral_angle_d4.9981560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.26281270.18312582X-RAY DIFFRACTION99.67
2.15-2.20.21921210.17892610X-RAY DIFFRACTION100
2.2-2.260.27061420.20642599X-RAY DIFFRACTION99.96
2.26-2.330.24571250.18532593X-RAY DIFFRACTION100
2.33-2.40.2091560.17822595X-RAY DIFFRACTION100
2.4-2.490.23011420.1822598X-RAY DIFFRACTION100
2.49-2.590.21911280.17982616X-RAY DIFFRACTION100
2.59-2.70.21511180.17962640X-RAY DIFFRACTION100
2.7-2.850.19921410.17612611X-RAY DIFFRACTION100
2.85-3.020.18891570.18462612X-RAY DIFFRACTION100
3.02-3.260.20741310.18152641X-RAY DIFFRACTION100
3.26-3.590.1721170.15962699X-RAY DIFFRACTION99.93
3.59-4.10.18421530.14772659X-RAY DIFFRACTION99.82
4.1-5.170.1691430.13542712X-RAY DIFFRACTION99.86
5.17-34.350.16151430.15872896X-RAY DIFFRACTION99.87
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)
11.447387670720.487194452431-0.05014581665633.782160666840.7048035347553.35306134066-0.2576933426640.1576529288730.533422802713-0.2125580049510.1512520493240.410301720495-0.743204399502-0.15088534751-0.0006927685450460.477864486072-0.0480119485283-0.1241244748990.1463708641430.0358437276680.41215635195451.67484531423.7154959363-24.5598754851
21.539083122110.03751523541230.1624922251314.93258844821-0.3117247915051.22296774378-0.07260978359480.06764904691470.0788799100624-0.06520769545630.0619543886435-0.146434122791-0.1660747554560.1179093450840.002252270736870.235395036134-0.0414430142763-0.006737621777930.126936859211-0.03775951021560.13398879926461.3034560913-10.7057157236-17.2903201689
34.41251951352-0.419925136306-1.124895992672.76190613504-0.238801151263.357861142180.0028098783657-0.203667188484-0.09267078841620.2880075109840.08268839279530.08378451725590.430951738127-0.204066897134-0.07549501271080.301964906332-0.05704044594340.006374368045310.155323298112-0.01905043036310.16693101517452.6745528817-26.194335009-9.40479653647
44.781818757950.526310112799-2.80125531483.2153092916-2.016196741565.83651680404-0.240945310439-0.101831925129-0.298705013858-0.05347234316670.0531067269564-0.3901985889890.4246866062770.5476480392710.202123827910.2246851737580.0288109452166-0.03190725073920.168181524864-0.09247185506560.18889548742767.1710100737-21.7651803985-14.3090532854
51.360958814110.2807604644990.8785987354151.827802397030.5597104285711.62295569719-0.1643715845050.2569872622480.00253590906481-0.0717022797050.203056464384-0.135373910059-0.1631197769210.406867190796-0.03472739974050.188731600506-0.07740521454370.0271686283760.180530926847-0.03041879129910.15313586410262.9330653902-14.673276853-21.3977367858
62.030583695340.823763485570.4907750774792.519133144640.4214616392840.801106075033-0.23557847991-0.02991695968060.243954455331-0.08968044464770.03410114269220.21915607767-0.361137139537-0.1762120775290.2019810936590.230283229265-0.0176082468456-0.01238022446820.099095897176-0.02460782848410.17913070374350.5027269121-8.35208979259-19.4453364648
72.81206069786-0.025090800391.958922748793.57780346457-1.725004563162.82475643291-0.2417366108040.1152718013310.24918671666-0.08428577177580.01159645461390.605143534098-0.74848252028-0.6978501750010.2522272218990.3383030111590.0593030588181-0.07672741284940.203792870186-0.07296742577920.35981026752943.6668542538-2.21528877888-19.5535908609
84.76819271069-0.1655301937950.2193745271382.43302074876-0.9766989506851.714015954530.230683053645-0.426993806028-0.009591864524250.320926708056-0.009029158826230.671706707260.259353824199-0.641080324638-0.1117005414360.425653696153-0.3756864538320.2041214988070.699191615233-0.2499765567810.54207323675221.2276351375-35.7001071417-22.0659378743
91.756824544731.0678140283-0.08220084060721.3623265879-0.2211069128691.726563398570.107062131471-0.103997971302-0.1293065471180.253336373791-0.1626863281190.2409131061960.27948507105-0.3291337350310.04582508174570.304676853898-0.1579360203520.06051461547110.230121141449-0.05297929497080.24785227937332.3944791449-36.2571378234-31.05501182
103.60359747225-1.56760260227-0.4765336746464.08652729371-0.08886969741711.85914701127-0.007984822538440.3106239739370.331362785173-0.176013567676-0.038754213180.0879197077133-0.3704839294520.0507409209150.06393932025410.256825619681-0.105637685776-0.03374226797290.2043575946860.01963729424940.22851855221241.7232941285-18.3439288084-45.2854525336
112.35527466735-1.059368372960.3487137353361.267322288290.6914930968192.75780002686-0.009278451233350.233592863390.031318901627-0.0580033604133-0.103030746987-0.0952922819530.05876210071860.1515246127120.08218652359010.215729831097-0.1176929595880.003490183340950.194040358724-0.03515976302340.15585173537443.8456358255-33.8756479296-47.7318224407
121.95251622250.694588885020.6154294694871.428356730660.4917112573811.583232794340.03332761248250.217133959471-0.1842190675710.07382470541220.06040672129950.09163142754170.272318370251-0.00989079327004-0.1143290980110.218399138988-0.09759077704840.009884497124880.174145944323-0.03263215772050.17084923120540.9990334317-36.2812801279-37.6255287613
133.891127877261.509758575043.033928887492.202573173881.230195369384.18453077048-0.0453161806526-0.03999815619640.2047547256780.0195274131696-0.2270825232240.3979176000740.0194362378609-0.5168537229390.2797776647480.164698654546-0.05445017137040.01068671807140.233083473358-0.07825595690760.25694732370832.6185845604-25.9073530724-32.7350639972
142.091145639930.7051277324470.1751186262462.621103471470.7377283189242.21514559430.0938505162077-0.1489583782240.00991250665860.210413174818-0.1916745003440.393349964530.0813800608234-0.334100232940.05979946721180.193327391068-0.1220892665450.06054277283340.23588310034-0.05854602782880.25422602532131.8858331612-30.4806809647-27.5348580293
151.818280830170.1822135604131.242640234562.63117492078-1.556510152573.179496060260.0439270158329-0.5016959933170.3598180156330.353662146971-0.09301125742830.662604876792-0.373479512727-0.733187989643-0.08149007133650.251866928068-0.08524814341780.1196398908660.440158246547-0.1682903894260.45234377213525.8952623314-25.5356097225-23.8599129014
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 24 through 58 )AA24 - 581 - 35
22chain 'A' and (resid 59 through 82 )AA59 - 8236 - 59
33chain 'A' and (resid 83 through 119 )AA83 - 11960 - 96
44chain 'A' and (resid 120 through 142 )AA120 - 14297 - 119
55chain 'A' and (resid 143 through 194 )AA143 - 194120 - 171
66chain 'A' and (resid 195 through 243 )AA195 - 243172 - 220
77chain 'A' and (resid 244 through 265 )AA244 - 265221 - 242
88chain 'B' and (resid 24 through 38 )BF24 - 381 - 15
99chain 'B' and (resid 39 through 82 )BF39 - 8216 - 59
1010chain 'B' and (resid 83 through 119 )BF83 - 11960 - 96
1111chain 'B' and (resid 120 through 142 )BF120 - 14297 - 119
1212chain 'B' and (resid 143 through 194 )BF143 - 194120 - 171
1313chain 'B' and (resid 195 through 218 )BF195 - 218172 - 195
1414chain 'B' and (resid 219 through 243 )BF219 - 243196 - 220
1515chain 'B' and (resid 244 through 265 )BF244 - 265221 - 242

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