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- PDB-7bh7: Room temperature, serial X-ray structure of the ertapenem-derived... -

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Basic information

Entry
Database: PDB / ID: 7bh7
TitleRoom temperature, serial X-ray structure of the ertapenem-derived acylenzyme of CTX-M-15 (10 min soak) 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 activity / beta-lactamase / 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
Chem-TVE / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)28,8294
Polymers28,2931
Non-polymers5363
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-21 kcal/mol
Surface area10980 Å2
Unit cell
Length a, b, c (Å)45.258, 45.975, 119.032
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-TVE / (2~{S},3~{R},4~{R})-3-[5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl]sulfanyl-4-methyl-5-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-2-carboxylic acid


Mass: 477.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N3O7S / 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: 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.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.8 %
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: 0.97 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: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→59.52 Å / Num. obs: 30691 / % possible obs: 100 % / Redundancy: 47.09 % / Biso Wilson estimate: 14.46 Å2 / CC1/2: 0.902 / R split: 0.244 / Net I/σ(I): 53.658
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 1492 / CC1/2: 0.258 / R split: 0.583 / % 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: MOLECULAR REPLACEMENT
Starting model: 6qw8

6qw8


Resolution: 1.65→59.52 Å / SU ML: 0.1446 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.3246
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1934 1550 5.05 %
Rwork0.1618 29141 -
obs0.1634 30691 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.18 Å2
Refinement stepCycle: LAST / Resolution: 1.65→59.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 26 202 2171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01152025
X-RAY DIFFRACTIONf_angle_d1.06052756
X-RAY DIFFRACTIONf_chiral_restr0.0665325
X-RAY DIFFRACTIONf_plane_restr0.0066361
X-RAY DIFFRACTIONf_dihedral_angle_d17.2824755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.24571430.21852601X-RAY DIFFRACTION99.89
1.7-1.760.25241270.19422599X-RAY DIFFRACTION99.96
1.76-1.830.22121480.17572603X-RAY DIFFRACTION100
1.83-1.920.19971330.16082616X-RAY DIFFRACTION100
1.92-2.020.20281230.15522638X-RAY DIFFRACTION100
2.02-2.150.19051420.15512629X-RAY DIFFRACTION100
2.15-2.310.15951400.14672634X-RAY DIFFRACTION100
2.31-2.540.17821200.1562666X-RAY DIFFRACTION100
2.54-2.910.20011550.15932645X-RAY DIFFRACTION100
2.91-3.670.19181680.15232673X-RAY DIFFRACTION100
3.67-59.520.18511510.16572837X-RAY DIFFRACTION99.97
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)
11.525192513991.3528913736-1.596176684351.89951181879-1.139983502752.57035717756-0.3280707686770.339710475121-0.468693087047-0.4925210375630.121142672136-0.4099209160140.504195537783-0.03182889985090.1633314232160.21819274935-0.01071659600380.07498712975480.179108384287-0.03500597231580.1726987283115.2992248628-20.84502008224.28733612099
21.840141301360.288416742947-0.281868244732.18462120122-0.09631441150341.19042763583-0.0320214454939-0.0739021505169-0.260554444776-0.04930406274680.0164309608783-0.2056050970680.1784491349630.1247996729960.05810160029410.1005187621620.02052512251650.01379666050550.1012982983990.0177359617050.09001096022984.6257382693-20.43687101415.0808408499
31.62896779434-0.272817597853-0.240720404291.7267776778-0.2448843784311.382360727880.00640421541312-0.3191771387150.1141867834260.335650896840.1065603360440.24660787242-0.0731324299053-0.0477644445966-0.04738950394880.155601680783-0.001481943165460.04356212459250.126506037747-0.006558219810070.116955863454-12.2097044194-5.8503309146129.8705516237
47.9439073861-2.72107125651-2.394158844398.35711464932.238041384166.416030235340.0407232036360.3691287641460.294584106885-0.557443075933-0.0959494723440.344529345554-0.437083328755-0.1405736074310.05342026109960.1665291788840.00646318929263-0.03439576098650.0925024600030.03416047606990.183089364956-15.83183101238.07514484518.8087692013
51.53527782455-0.272355298388-0.2677517057221.484449002410.2976261647420.8303442963280.0289497326035-0.03327723744580.06579866338150.0222237470542-0.009086319597360.0125269071341-0.02758929447040.0173427806033-0.03070705805470.0871255133891-0.008389668981470.002906383343550.0749378809613-0.003793110160980.0539529485295-3.16534392443-6.0079169386123.1498385409
62.66743199514-0.3173447186080.2493567779421.579855377280.2140643764342.93983659650.0249116528256-0.159827328761-0.2639143683410.1855187549430.06676624891040.2437434859560.085499196692-0.177393339956-0.03814117581650.117060780509-0.01644401701520.01366134114570.1017694078310.01266362930550.113976261656-14.5018046064-17.006139410125.8984107099
71.52194332730.1840774504470.002091586474791.111442809360.2003620254631.511033259060.01038224985210.119845229577-0.00178933674827-0.1460664029310.01251517420460.1403164555520.00993641849365-0.102834150759-0.02067648181140.09175875505540.00143874722708-0.01223236177450.08683376832470.004364562382360.0782592413861-8.96585608754-14.64206479079.80391441034
85.472062766153.81480466703-2.078346786765.57107028102-2.527648755562.89561941641-0.03372166826640.158327039508-0.242088648723-0.2158961988090.1194754217610.05709855532220.288955175607-0.111251548918-0.05682036675670.135396632420.0129975945074-0.01833284327950.0874285603425-0.005901194403820.0946197256214-5.86515986959-22.315809103212.1221072463
95.307213658513.20907667175-0.6342852631556.89115929108-0.9727754248573.07878308904-0.1475627915860.3810629311990.148808270442-0.5228203234790.2367445591690.2507212928680.0807592524968-0.0442879600659-0.1012112591370.1330952623290.01090056362690.01764958856980.1503882679620.01024678101450.0321262097986-0.603670679499-12.73492861392.32477740546
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 51 )28 - 511 - 24
22chain 'A' and (resid 52 through 68 )52 - 6825 - 41
33chain 'A' and (resid 69 through 96 )69 - 9642 - 70
44chain 'A' and (resid 97 through 115 )97 - 11571 - 89
55chain 'A' and (resid 116 through 194 )116 - 19490 - 171
66chain 'A' and (resid 195 through 213 )195 - 213172 - 190
77chain 'A' and (resid 214 through 250 )214 - 250191 - 229
88chain 'A' and (resid 251 through 264 )251 - 264230 - 243
99chain 'A' and (resid 265 through 287 )265 - 287244 - 266

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