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- PDB-5dtk: Fragments bound to the OXA-48 beta-lactamase: Compound 17 -

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Basic information

Entry
Database: PDB / ID: 5dtk
TitleFragments bound to the OXA-48 beta-lactamase: Compound 17
ComponentsBeta-lactamase
KeywordsHYDROLASE / inhibitor / complex / fragment / lactamase
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3,5-di(pyridin-4-yl)benzoic acid / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.60000241571 Å
AuthorsLund, B.A. / Christopeit, T. / Leiros, H.-K.S.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Screening and Design of Inhibitor Scaffolds for the Antibiotic Resistance Oxacillinase-48 (OXA-48) through Surface Plasmon Resonance Screening.
Authors: Lund, B.A. / Christopeit, T. / Guttormsen, Y. / Bayer, A. / Leiros, H.K.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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

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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
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,74223
Polymers121,7594
Non-polymers1,98319
Water23,0411279
1
A: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,77810
Polymers60,8792
Non-polymers8988
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint6 kcal/mol
Surface area20130 Å2
MethodPISA
2
B: Beta-lactamase
hetero molecules

C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,96413
Polymers60,8792
Non-polymers1,08511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_647-x+1,y-1/2,-z+21
MethodPISA
3
C: Beta-lactamase
hetero molecules

B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,96413
Polymers60,8792
Non-polymers1,08511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y+1/2,-z+21
Buried area3450 Å2
ΔGint11 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.523, 124.310, 108.742
Angle α, β, γ (deg.)90.000, 98.263, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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, blaOXA-48, KPE71T_00045 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-5F3 / 3,5-di(pyridin-4-yl)benzoic acid


Mass: 276.289 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H12N2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1279 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.82 % / Description: Plate-like appearance, but some thickness.
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 8-12% PEG8000, 4% butanol / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.478→49.38 Å / Num. obs: 195258 / % possible obs: 98.02 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.0316230801 Å2 / Rmerge(I) obs: 0.08237 / Net I/σ(I): 9.67
Reflection shellResolution: 1.478→1.531 Å / Redundancy: 2.2 % / Rmerge(I) obs: 1.033 / Mean I/σ(I) obs: 0.82 / % possible all: 85.02

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
PHASER2.5.6phasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR
Resolution: 1.60000241571→49.3793661959 Å / SU ML: 0.154609913625 / Cross valid method: FREE R-VALUE / σ(F): 1.35792690821 / Phase error: 17.9583134376
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.172474668469 1687 1.07524140349 %Random selection
Rwork0.145573684921 155208 --
obs0.145862928729 156895 99.7799556095 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.0672524111 Å2
Refinement stepCycle: LAST / Resolution: 1.60000241571→49.3793661959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7944 0 138 1279 9361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008443939364418457
X-RAY DIFFRACTIONf_angle_d0.94936966952811456
X-RAY DIFFRACTIONf_chiral_restr0.05793569641161189
X-RAY DIFFRACTIONf_plane_restr0.006516534929921568
X-RAY DIFFRACTIONf_dihedral_angle_d23.50107546643141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64710.3220301105321410.27845641995712937X-RAY DIFFRACTION99.7254842153
1.6471-1.70030.2410604860041400.24476415607512883X-RAY DIFFRACTION99.7778118296
1.7003-1.7610.2363459789841400.21193609331312883X-RAY DIFFRACTION99.5794463985
1.761-1.83150.2340560094591400.19605874826512898X-RAY DIFFRACTION99.778066886
1.8315-1.91490.1934959799641400.16934592704612893X-RAY DIFFRACTION99.8467785183
1.9149-2.01590.159795829951400.14884161008912897X-RAY DIFFRACTION99.8238897397
2.0159-2.14220.157979912371410.13382690199512970X-RAY DIFFRACTION99.7717068716
2.1422-2.30750.1512187348521410.12570528275512900X-RAY DIFFRACTION99.8315853939
2.3075-2.53980.134770849611410.12336461647212965X-RAY DIFFRACTION99.9085226406
2.5398-2.90720.1672801776821400.12558574876512924X-RAY DIFFRACTION99.85477337
2.9072-3.66260.1751885610091410.12885629858812998X-RAY DIFFRACTION99.9011557178
3.6626-49.40290.1526285564651420.13311098087213060X-RAY DIFFRACTION99.5625942685
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.772661337110.584189761321-2.721925089022.735689343710.1084286129633.853257316530.167626722112-0.210059258410.2729995105060.214248388379-0.0494647453251-0.11003284544-0.3032840719230.299172246146-0.1358892135190.155869909468-0.0388921574786-0.02306338739840.139566367183-0.02237776050670.1494827161459.4783334153952.6371089231164.032472669
20.4773657851690.177402618694-0.159605657350.995613470677-0.005421943398531.10808311692-0.02377373658460.0461455283953-0.00224019526883-0.0963460164345-0.002538958386760.09357203300220.0571936339913-0.06784544634950.03549069774220.145486736251-0.00550375963736-0.001781739867760.141737560584-0.002312691553590.132837076915-4.6033547706437.2685559987145.736802261
30.5751099908150.3908448843110.0348742021691.79176869787-0.5030970578451.214089908670.0253366018047-0.02974238520280.04474197400160.0983393081596-0.0007347103299370.185430323279-0.0610890462412-0.108651787585-0.01172144866590.109880714030.008129218734750.02123459499530.130421969886-0.007518325386910.140088713075-6.883403670441.676618364156.738508689
41.343409020650.592998027175-0.7547029173992.39317469009-0.698509941452.172282330390.0624636214041-0.0765452552469-0.02073006069330.106548778257-0.0773260919064-0.136533549984-0.005043041517950.1999802414030.01416368444320.08300783899850.00136375929528-0.001175190693690.107963576232-0.002340778633510.1062459207098.5511281391942.1227961566158.444699791
56.4240196465-0.834551449483-2.218310986253.55514225251-0.04734570138553.768066210410.1233798119860.1681893346410.338162839917-0.32796017569-0.03328691872780.364357728813-0.185764030723-0.396880447074-0.1277337045180.1994353966790.0301968107163-0.06485939844960.158325377485-0.0009201954173180.206762118483-5.4339888440221.8711195184104.158314927
61.95781833642-1.432482291120.1931774064682.81552806459-0.202427204341.10708427549-0.0167117674221-0.06359782450560.002708759371510.248640465343-0.006126366441890.08750046814410.0438123664403-0.02487142070650.03908520564430.209800320826-0.0166163190888-0.004631468525760.124827479881-0.0253228125370.1202953434284.2865232397216.7474272438119.389217742
72.620603364710.140188559277-1.481809944030.934185959471-0.641424468462.46215546158-0.15067905412-0.2504859471440.111505294550.7091200063740.09000590398550.1492609686490.432695504375-0.1924806163020.09261885147850.4698619347630.003845693148340.05742677540880.2354874080140.002647533684340.1639337510445.91017100485-0.923555923279129.863054958
80.625399797552-0.391895592628-0.02253738700971.714627657540.5246623131491.33616854671-0.0255060629206-0.136334887251-0.02739202887510.550834821019-0.0105150062544-0.0196958911920.177042658480.02497236164510.05208111558910.3068830683210.008262661335010.0005064280843610.151116510873-0.003987137306920.1219637299047.435411349989.69445734935126.753213519
90.793374249947-0.348819057208-0.06511566857811.922672437520.6306770361621.166400778670.0253693906645-0.007446280931630.01794753667860.0612722411398-0.06238211045260.1091418454530.0143596991351-0.09463133381390.04462093652860.161813018047-0.0162243398866-0.003349388326970.1104576458-0.007890221009510.1147489534453.0727925586712.3324139125113.473300587
102.768589378-0.366597714805-1.272050919153.21414343887-0.4830002020637.958059571260.06473437867560.243689318722-0.244981519647-0.243717882722-0.1344445969230.4436689890470.333697984993-0.6405179290730.07756500012970.152551416706-0.0236923015167-0.04612909737150.212198827591-0.07150940331630.287016226771-10.191015166711.7546050273106.921287009
113.85123218573-1.587860294861.388829356254.36406390104-1.040468661424.555201857050.02517607334450.041999352169-0.129782084208-0.362829754595-0.0192324628275-0.5033410119330.2361525176060.243436227549-0.03103583969060.2027146756960.02242645926410.05608797942670.110776266879-0.02028272542630.22952043956216.217440335335.9423098248107.126238273
121.62662650597-1.30815231967-0.2350183459622.83844513517-0.04184104295880.9833236996470.0265013930613-0.00561023288096-0.0541588960177-0.0516377416926-0.02632312138010.03996958565090.05414580608590.009278009770110.006253339848810.155666893737-0.00864954562062-0.006462162373810.111636181856-0.006244420689790.1184257486071.7593744604743.4577537811116.454052859
131.269153828550.7700848113170.7209174336890.771205975855-0.2287144356183.952210369190.0414086154496-0.0694747478408-0.020874057090.184693969726-0.01238195587620.0705330719835-0.3247787492160.1269870252710.004446869007750.2496071962020.02919674148810.02020202278040.153572538525-0.01664646337020.164953514166-1.2895297535561.7553743528125.569648299
142.88619665318-1.98000279375-2.059644385263.67962993328-1.630406281015.586313336750.0391538237129-0.177567602176-0.01750646304230.165444875868-0.185849774012-0.0792653456633-0.2007329083250.2943576942540.1535900640410.181395466787-0.0178089981983-0.01641193127530.1353033563660.004591018766550.1198839803076.0152819440859.7779112346124.135396071
154.688567294911.460761004451.840151841614.322656957562.842298466954.766221479570.0111825943424-0.101882301551-0.04129143033150.0684327426813-0.03869302053060.306917394157-0.0865666565699-0.2934131249560.02775391509190.1472062770340.008902444556940.01871619583630.12022806940.03649585066950.150291819665-8.5688649002950.0484112193121.423196237
160.5975921348970.119142401017-0.2254254265091.74832449376-0.790766199631.03474785163-0.01742381669690.0431101257714-0.0521126528093-0.1787073860440.02574847569850.1251803964790.114377988452-0.08121807653-0.004749729860880.1794740105530.000172395042404-0.01580499486880.1245385615-0.0151959554810.133636005687-2.1694358802745.7512204092112.735208364
170.8330821660030.1518736319350.0009947466476132.76646918872-1.411820834472.282506524020.003649488964920.00258442701413-0.00706903749976-0.130867223275-0.065645836976-0.1230788490530.1102762961780.07575592331790.05792215477190.1480940985560.01105716515240.008514045850420.109687102932-0.007051246570530.13370685526511.866323212346.9931964646112.832247228
182.073065998160.120234183956-0.4877089047653.53707844078-1.264511917854.24070202999-0.009254921905260.121680661236-0.0143455936509-0.249908720842-0.116211109118-0.4187531470320.09160035520970.4929195029170.2004903784210.1447957877170.02063916052140.01348264129470.1742459460310.03262892780460.24102223181620.843869554545.2748756163111.847238793
196.240478946360.9625692268472.952614887113.779927496811.604742359025.85360005310.009896475731260.180634596309-0.362648016678-0.0536932408206-0.02119260749630.07199143958310.2682564592820.257851570958-0.03060618681170.2092975912550.03112732679110.04077741435360.1327598161840.03777810301060.29014773097515.30216984072.72415174036162.098040089
207.30173476224-2.151719900474.855368238864.06392233335-1.590791894896.80512240903-0.003590939990.0682431407027-0.225336492916-0.160199792224-0.0379972690575-0.09918054837840.1708772802420.0915564552945-0.02340805882980.133073960154-0.002288045609250.05943200826740.07629809616320.001456175709190.1340514399258.158213601415.32783627187160.175259397
212.10409586212-0.781122344404-0.3661249549742.15523140573-0.3229032782491.6444083034-0.122283535613-0.0625846549577-0.1185066937090.326724394934-0.00100956952907-0.02742194748140.08707981605320.04175732779920.1366295723580.207510375512-0.03537978037990.03471471599240.1164207786070.01646908553150.127275486128-1.684722567319.97692300517173.297018375
224.177201499590.1736055674562.431567917490.5433730638670.7308642900833.92129679317-0.0456431566276-0.329472195753-0.02524232949420.5341338335090.0411394659127-0.0164573016411-0.3995324555940.05386044577430.03029564760320.454174539128-0.0154114006920.03040388762120.1894926055060.0003253737124580.156326346759-4.9162786186827.8627986496183.13862938
233.56466625449-1.90551242363-0.8848921066693.0033269696-0.3189367704484.13778216573-0.00310253391331-0.1385200654280.1546161664540.487892504473-0.107691575003-0.177556304563-0.198745692350.1450710150040.1164245608840.287017848902-0.038057087892-0.006573622493780.131116939079-0.0008751328458660.1234330333871.9348518576326.4676773488179.836839085
242.70716093411.025337989120.4597311536632.77629864411.355543961162.849924661750.0829799150705-0.1149327075630.03396700086880.458540293482-0.06298776945620.262797772033-0.0490307962163-0.252835406238-0.01899640480270.268336496184-0.01130133592580.07506368293650.1441183828290.02807388262940.141192083696-11.743957826315.1670728115180.071217989
250.6183930626110.051607019909-0.1530598868431.64664270785-0.6860530590461.345740702650.00177122946268-0.0602507293169-0.04670597782920.122254636023-0.0744637272673-0.04163244656550.07347859052980.04360162449970.07432489335480.156601121434-0.02225450867520.02078985640470.0977412224210.002752736322430.0998813208292-0.022949042054113.3360911544169.282781969
262.54907953198-0.140250080477-0.4563005144893.726532240750.5383624643736.933799514320.09631426414090.04472547286290.03977079136080.0846560133088-0.0309908001945-0.319409302766-0.1442302655750.360680216729-0.06313330767120.148165266591-0.0167482753132-0.001430070835830.1800027253830.06240340142010.24861387253415.746560892613.9667665866164.916714931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 58 )
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 155 )
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 194 )
4X-RAY DIFFRACTION4chain 'A' and (resid 195 through 265 )
5X-RAY DIFFRACTION5chain 'B' and (resid 23 through 58 )
6X-RAY DIFFRACTION6chain 'B' and (resid 59 through 82 )
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 102 )
8X-RAY DIFFRACTION8chain 'B' and (resid 103 through 155 )
9X-RAY DIFFRACTION9chain 'B' and (resid 156 through 243 )
10X-RAY DIFFRACTION10chain 'B' and (resid 244 through 265 )
11X-RAY DIFFRACTION11chain 'C' and (resid 23 through 58 )
12X-RAY DIFFRACTION12chain 'C' and (resid 59 through 82 )
13X-RAY DIFFRACTION13chain 'C' and (resid 83 through 102 )
14X-RAY DIFFRACTION14chain 'C' and (resid 103 through 119 )
15X-RAY DIFFRACTION15chain 'C' and (resid 120 through 141 )
16X-RAY DIFFRACTION16chain 'C' and (resid 142 through 194 )
17X-RAY DIFFRACTION17chain 'C' and (resid 195 through 243 )
18X-RAY DIFFRACTION18chain 'C' and (resid 244 through 265 )
19X-RAY DIFFRACTION19chain 'D' and (resid 23 through 38 )
20X-RAY DIFFRACTION20chain 'D' and (resid 39 through 58 )
21X-RAY DIFFRACTION21chain 'D' and (resid 59 through 82 )
22X-RAY DIFFRACTION22chain 'D' and (resid 83 through 102 )
23X-RAY DIFFRACTION23chain 'D' and (resid 103 through 119 )
24X-RAY DIFFRACTION24chain 'D' and (resid 120 through 141 )
25X-RAY DIFFRACTION25chain 'D' and (resid 142 through 243 )
26X-RAY DIFFRACTION26chain 'D' and (resid 244 through 265 )

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