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- PDB-7bh6: Room temperature, serial X-ray structure of CTX-M-15 collected on... -

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Basic information

Entry
Database: PDB / ID: 7bh6
TitleRoom temperature, serial X-ray structure of CTX-M-15 collected on fixed target chips at Diamond Light Source I24
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / serial crystallography / beta-lactamase / antibiotic / ertapenem
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic / membrane
Similarity search - Function
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsHinchliffe, P. / Tooke, C.L. / Butryn, A. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J014400/1 United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography.
Authors: Butryn, A. / Simon, P.S. / Aller, P. / Hinchliffe, P. / Massad, R.N. / Leen, G. / Tooke, C.L. / Bogacz, I. / Kim, I.S. / Bhowmick, A. / Brewster, A.S. / Devenish, N.E. / Brem, J. / Kamps, J. ...Authors: Butryn, A. / Simon, P.S. / Aller, P. / Hinchliffe, P. / Massad, R.N. / Leen, G. / Tooke, C.L. / Bogacz, I. / Kim, I.S. / Bhowmick, A. / Brewster, A.S. / Devenish, N.E. / Brem, J. / Kamps, J.J.A.G. / Lang, P.A. / Rabe, P. / Axford, D. / Beale, J.H. / Davy, B. / Ebrahim, A. / Orlans, J. / Storm, S.L.S. / Zhou, T. / Owada, S. / Tanaka, R. / Tono, K. / Evans, G. / Owen, R.L. / Houle, F.A. / Sauter, N.K. / Schofield, C.J. / Spencer, J. / Yachandra, V.K. / Yano, J. / Kern, J.F. / Orville, A.M.
History
DepositionJan 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4474
Polymers28,2931
Non-polymers1553
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-38 kcal/mol
Surface area11130 Å2
Unit cell
Length a, b, c (Å)45.280, 45.958, 118.486
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-lactamase


Mass: 28292.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaCTX-M-15 / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: G3G192, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulphate, 0.1 M Tris 8.0

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Data collection

DiffractionMean temperature: 294 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98194 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98194 Å / Relative weight: 1
ReflectionResolution: 1.65→59.24 Å / Num. obs: 30552 / % possible obs: 100 % / Redundancy: 61.27 % / Biso Wilson estimate: 13.95 Å2 / CC1/2: 0.893 / R split: 0.254 / Net I/σ(I): 47.659
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 11.15 % / Mean I/σ(I) obs: 6.38 / Num. unique obs: 1491 / CC1/2: 0.569 / R split: 0.488 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6QW8

6qw8


Resolution: 1.65→59.24 Å / SU ML: 0.1304 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.3495
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1972 1543 5.05 %
Rwork0.1629 29006 -
obs0.1646 30549 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.46 Å2
Refinement stepCycle: LAST / Resolution: 1.65→59.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 7 222 2173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862036
X-RAY DIFFRACTIONf_angle_d1.03062771
X-RAY DIFFRACTIONf_chiral_restr0.0583321
X-RAY DIFFRACTIONf_plane_restr0.0075367
X-RAY DIFFRACTIONf_dihedral_angle_d20.573765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.24931430.20842591X-RAY DIFFRACTION100
1.7-1.760.21961290.19182587X-RAY DIFFRACTION100
1.76-1.830.22891420.17062581X-RAY DIFFRACTION99.96
1.83-1.920.21281320.15972604X-RAY DIFFRACTION100
1.92-2.020.16651240.15392622X-RAY DIFFRACTION100
2.02-2.150.21271410.1512616X-RAY DIFFRACTION100
2.15-2.310.16981390.15112632X-RAY DIFFRACTION100
2.31-2.540.22241190.15482659X-RAY DIFFRACTION99.96
2.54-2.910.16831550.15832624X-RAY DIFFRACTION100
2.91-3.670.22221680.15362660X-RAY DIFFRACTION100
3.67-59.240.17541510.17422830X-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)
11.91030978060.869081116959-0.6576162986981.8077393259-1.33165055791.86498434132-0.1255758596440.191781418643-0.254924990706-0.3400870250990.046640229024-0.2821700752920.2946303138270.08445810197250.07976946464630.1195790005070.007519638643860.03670639305540.139508033128-0.01339360376320.1228733097225.13812342702-20.67840445498.39844614276
22.56869300491-0.794023386804-0.566304610352.72371438764-0.2653177688032.0724730901-0.0796229326801-0.3124407809050.09330758798060.3026868100470.1337621170950.2022978846530.0830332103258-0.0497752442253-0.0195793007140.0734915065958-0.0263798361640.006192685884450.128323342768-0.01648763227970.105541704768-12.4460043418-5.5465463371829.7866936909
37.4185110601-2.47118212815-1.992259626216.807158692652.860070792353.95266731251-0.06835989934590.3236381428640.366054260721-0.5444264967030.0008531279240290.432494606014-0.356858200427-0.2840439969420.05025979571070.1409756919880.0201712864351-0.04963190000310.1376672622460.04808323804680.180917812104-15.80359079647.7476260293318.6293108456
40.654992886953-0.309752061159-0.1818729490331.905165522940.109476229420.894488647655-4.32024171181E-5-0.02812911352650.03349654863640.0293432618670.004420354831510.03073644932-0.01822421786690.0124841384137-0.00251579986710.0469111134756-0.01012888017740.0006762219837940.0829185342634-0.003875338465140.0600667248136-3.20056109106-6.4623184378723.1425619386
53.7771708407-1.505552069290.1471844406112.419749418470.3195886177653.41733165601-0.0306129397344-0.0314064792422-0.2368550355220.1574838009340.05409746343770.1967965050990.114666102419-0.225836796948-0.06388231365860.0552824145568-0.03194129849190.01435870747460.1034738322410.01476582056940.122977019329-14.5104525346-17.290028766825.8146977904
60.820753179081-0.066578845474-0.05476231646121.790569519010.3041160154971.831049471290.05623970100380.0494211993678-0.029365063978-0.144143496744-0.06337733957070.1503953114050.000108963817941-0.1473807121690.007610532822950.0495150846207-0.000234888044969-0.01513469943310.09223621620810.003997452284770.0794374687003-9.06783934433-14.87243513529.69283230326
76.182733075894.46951351523-2.724257889215.4217487534-3.169785943883.26408453303-0.07608214586950.20043552702-0.288775888309-0.2883516248610.1391513406880.007023178069450.277874379643-0.109797731558-0.04573951140290.09533099351940.0182616393763-0.01761580266050.0743513287433-0.01384771009480.0933222631457-5.93224390768-22.503386335811.9664754358
85.037679588743.7447806229-1.025224679577.47212002116-2.01142715942.95483665567-0.1276386407670.2918888207820.216749392864-0.5065885169850.2194194319250.2428110215520.04478294840880.0404793275673-0.1048902806410.1101802547760.002589327019750.01726804765850.138892064388-0.009940906002760.0335128211865-0.682865418167-12.54623403052.27616612314
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 68 )28 - 681 - 42
22chain 'A' and (resid 69 through 96 )69 - 9643 - 74
33chain 'A' and (resid 97 through 115 )97 - 11575 - 95
44chain 'A' and (resid 116 through 194 )116 - 19496 - 180
55chain 'A' and (resid 195 through 213 )195 - 213181 - 199
66chain 'A' and (resid 214 through 250 )214 - 250200 - 237
77chain 'A' and (resid 251 through 264 )251 - 264238 - 251
88chain 'A' and (resid 265 through 286 )265 - 286252 - 275

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