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- PDB-7s5s: CTX-M-15 WT in complex with BLIP WT -

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Basic information

Entry
Database: PDB / ID: 7s5s
TitleCTX-M-15 WT in complex with BLIP WT
Components
  • Beta-lactamase
  • Beta-lactamase inhibitory protein
KeywordsPROTEIN BINDING / Beta-lactamase / antibiotic resistance / Beta-lactamase inhibitory protein / protein complex
Function / homology
Function and homology information


regulation of beta-lactamase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / extracellular region / membrane
Similarity search - Function
Beta-lactamase-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / BamE-like / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Beta-lactamase / Beta-lactamase inhibitory protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Streptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLu, S. / Palzkill, T. / Hu, L.Y. / Prasad, B.V.V. / Sankaran, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32956 United States
CitationJournal: Nat Commun / Year: 2022
Title: An active site loop toggles between conformations to control antibiotic hydrolysis and inhibition potency for CTX-M beta-lactamase drug-resistance enzymes.
Authors: Lu, S. / Hu, L. / Lin, H. / Judge, A. / Rivera, P. / Palaniappan, M. / Sankaran, B. / Wang, J. / Prasad, B.V.V. / Palzkill, T.
History
DepositionSep 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 inhibitory protein


Theoretical massNumber of molelcules
Total (without water)45,5672
Polymers45,5672
Non-polymers00
Water13,872770
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-9 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.480, 81.860, 129.120
Angle α, β, γ (deg.)90.000, 95.943, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

21B-230-

HOH

31B-471-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 28010.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaCTX-M-15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7S9T0, beta-lactamase
#2: Protein Beta-lactamase inhibitory protein / BLIP


Mass: 17556.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35804
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% w/v PEG3350, 0.2 M NaF, 0.1 M Bis-Tris-propane pH 6.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.4→33.49 Å / Num. obs: 94955 / % possible obs: 98.37 % / Redundancy: 1.9 % / Biso Wilson estimate: 9.75 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.8
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.057 / Num. unique obs: 511

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HBT and 3GMU

4hbt

3gmu


Resolution: 1.4→33.49 Å / SU ML: 0.0994 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.6787
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1663 2000 2.11 %
Rwork0.1512 92955 -
obs0.1516 94955 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.27 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3194 0 0 770 3964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583251
X-RAY DIFFRACTIONf_angle_d0.94664415
X-RAY DIFFRACTIONf_chiral_restr0.0856507
X-RAY DIFFRACTIONf_plane_restr0.0076575
X-RAY DIFFRACTIONf_dihedral_angle_d5.7798459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.17831410.16676549X-RAY DIFFRACTION96.8
1.43-1.470.20281400.16366516X-RAY DIFFRACTION97.22
1.47-1.520.18251410.15856547X-RAY DIFFRACTION97.44
1.52-1.570.1771400.15446542X-RAY DIFFRACTION97.69
1.57-1.620.17421430.15196597X-RAY DIFFRACTION97.94
1.62-1.690.18491420.14746602X-RAY DIFFRACTION98.07
1.69-1.760.16371430.15436655X-RAY DIFFRACTION98.45
1.76-1.860.17091430.15296644X-RAY DIFFRACTION98.55
1.86-1.970.17041430.14726644X-RAY DIFFRACTION98.88
1.97-2.130.15161430.14136690X-RAY DIFFRACTION99.04
2.13-2.340.16471450.14576700X-RAY DIFFRACTION99.36
2.34-2.680.16331450.15566749X-RAY DIFFRACTION99.58
2.68-3.370.16081450.15316767X-RAY DIFFRACTION99.75
3.37-35.990.15931460.14976753X-RAY DIFFRACTION98.18
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)
10.404593766202-0.258135272933-0.1291280854621.513087534780.3713934253730.598740265421-0.0166301750071-0.159115835571-0.1309094851060.358022241870.105267284149-0.06145731044790.2178984422570.06489033540940.006345075337510.1544348942640.00898687474007-0.02984356029230.08361660073580.02682910705650.08987027854744.54917380803-38.7732513764-15.4013465242
20.546805067018-0.1893580620790.09113653091770.348346581974-0.134060275490.576963335758-0.0111287077675-0.04532136993490.04342448795340.1278902540660.000349300960731-0.09143451888-0.1165541496150.09047680928750.028057652030.114065544769-0.0150196341094-0.01463797284790.0853756036631-0.009032681957170.08496573069865.49364141921-20.9180061835-21.186086197
30.488118040413-0.1041783420990.127817403261.935922393041.514769558072.483728542740.04567829961950.08632621865870.323924705795-0.0995212829496-0.02023581409850.106239202686-0.4281114360470.04367487902680.03222281826420.1542559617890.004888548008370.02199413272050.0673217463048-0.01607053589560.154567885556-3.91661434626-5.30688565227-38.4695492152
40.7160112478150.137370865737-0.1497082235970.703385088907-0.2224074994061.370896163560.01636923521220.09850582121260.0296438681239-0.08768663259490.02840682255680.0714446283103-0.042006412092-0.1164956150240.004707558929930.07447359080450.0144379077317-0.003711029178420.0794504276926-0.001713559274290.0910995670076-8.44281609312-14.774844332-38.2868894537
50.40994549774-0.112266538414-0.07042439005910.527706333837-0.2977317753210.3960146048830.0214774501021-0.05086117789670.04767649005840.0824424754729-0.046776323666-0.076823432739-0.05915646827650.0680877479660.02970808405050.0758588289359-0.00912242471585-0.00683032210040.06671897844540.000985868813080.08507939861977.71225866135-19.3160408993-29.3965965176
61.72493767209-0.6823024419590.5826601859541.25622613258-0.409133415071.34993935418-0.0775664172299-0.319772188323-0.03561292349990.2942055462660.1458703514080.1295254658-0.341395337317-0.175154760010.08186750840310.1787498874870.001307218947320.02511902316020.101467097607-0.02153638304290.0798338230095-3.7782079358-11.0161717269-18.871934449
70.612333021548-0.0387529926541-0.08449434129530.8045353671650.09892690859980.6938998761850.0172875450958-0.00434038282193-0.01677166657530.0187585207597-0.01411063125040.137430902576-0.0567555764928-0.206099423415-0.008588094898030.07508018748010.0008052148975760.008583634307160.09408897101920.008436642869760.0734315567553-5.86863602911-27.6113845743-21.6709875987
80.92489092225-0.480424107596-0.5362751398551.673898843621.087322569622.366080214340.113370784044-0.0226474680271-0.03616140543540.0096584476463-0.0682828589017-0.04584047326310.0130631592566-0.1935335528760.02601151643250.0822972814613-0.00129260166994-0.009785020916330.08122118191560.0157697953780.0548520879244-0.896450409307-32.1955754776-21.5702467934
91.862602906080.1172141426771.054254869391.963284018210.5337594977023.581615463210.0304438345069-0.268312775189-0.07245534230740.3215871540610.03378663519190.1035003090870.0325055867692-0.328662225430.01188084841280.135039995851-0.006981531066720.01388752519120.1038621376560.02238980282270.0750825620295-4.11164848081-35.3486296446-15.4287277224
101.63991577425-1.177880008331.815684656931.84764315110.1945238874374.484607941690.0149385808622-0.0538226255481-0.1018080360920.113578117711-0.02982106319170.1947532427970.112597778947-0.160259753943-0.0958953819190.0709553785933-0.009695971509467.01041063498E-50.06421561840090.004490629651710.105711427323-21.9861841345-32.6400922046-44.3058046939
111.098166669410.166179101506-0.4246839618160.604104132529-0.7630799235481.161930800030.05177577354460.01495846192150.05553392682690.007957814230970.06482072382570.1030172342870.0387163445701-0.0915780429295-0.04960891865210.0550666883051-0.002820121593020.002811396578750.06561605024570.01245636781780.0868712510047-28.5656678037-24.4959686174-46.7121286587
120.849052339165-0.4587756668520.02229465428150.590954845947-0.07116285916620.339322245485-0.0380782383292-0.144541897314-0.02555323341440.06561449262620.06542502109020.0495291505081-0.0433062687327-0.0299603031322-0.02228197323130.06638358885390.012887649693-0.005252679589640.0624170854841-0.0007221324587740.0698311916924-18.333500201-24.0748415877-36.2067333857
130.759104512086-0.083472932382-0.2772813675051.073571819480.05371907503170.8692131120270.0379747723340.0498400604218-0.0155821290081-0.0387458409503-0.05181573968660.04955980399910.02125846599730.0119084986462-0.02037985092490.0421957877650.003262884296270.0005042374787350.05123433130620.000580136525360.057267943977-17.2339050758-24.324820707-48.2681944262
141.19070256963-0.623568965250.7658255254951.23489060337-0.5583668713341.187897566030.0519446503420.145961780656-0.149100909485-0.195912329735-0.1324906944910.01338917114110.1404485797760.12457804873-0.005424092953320.1051589125640.0230625740620.02033135577720.194101773194-0.005164488792980.0868098862503-0.784569509847-25.6487510228-62.6057868514
150.948320649833-0.2129188318210.3690986602220.6578465426-0.3909771754020.604048961139-0.006158752514050.0685799947333-0.061951512018-0.0545088324358-0.0330877127679-0.08615136364440.03149281720940.0808698399825-0.007802655114570.06677472599340.004745430475770.008245375788140.08498609933560.004168520147240.063429746245-13.4407921617-21.8649213311-55.2903691899
160.8930769151020.2780708461710.2031462163360.09623837252250.06477888350621.81316755378-0.0400284203602-0.182950894458-0.06377295916220.0418986519077-0.0934757575767-0.1853383427390.2765482556030.319041651367-0.01219004829430.1445123548760.04562050188210.01691937230860.1768273580210.01988529063330.168323423288-2.20046383542-34.8086247504-44.8015598934
171.99723302534-0.5595820410.8009846506711.28743538634-0.7198258592471.750360004450.007381962004160.00972963392281-0.128372912270.0407858205997-0.0371914129490.01472367687420.01426511556290.2569076105410.02478585242270.05016605534880.009409211173630.006507331349950.1394067139520.006550775034670.0521456805805-1.51670619125-21.8465922817-54.588423308
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 27 through 51 )AA27 - 511 - 25
22chain 'A' and (resid 52 through 86 )AA52 - 8626 - 60
33chain 'A' and (resid 87 through 101 )AA87 - 10161 - 75
44chain 'A' and (resid 102 through 129 )AA102 - 12976 - 103
55chain 'A' and (resid 130 through 194 )AA130 - 194104 - 168
66chain 'A' and (resid 195 through 213 )AA195 - 213169 - 187
77chain 'A' and (resid 214 through 250 )AA214 - 250188 - 224
88chain 'A' and (resid 251 through 273 )AA251 - 273225 - 247
99chain 'A' and (resid 274 through 288 )AA274 - 288248 - 262
1010chain 'B' and (resid 1 through 11 )BB1 - 111 - 11
1111chain 'B' and (resid 12 through 25 )BB12 - 2512 - 25
1212chain 'B' and (resid 26 through 52 )BB26 - 5226 - 52
1313chain 'B' and (resid 53 through 84 )BB53 - 8453 - 84
1414chain 'B' and (resid 85 through 104 )BB85 - 10485 - 104
1515chain 'B' and (resid 105 through 132 )BB105 - 132105 - 132
1616chain 'B' and (resid 133 through 145 )BB133 - 145133 - 145
1717chain 'B' and (resid 146 through 165 )BB146 - 165146 - 165

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