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- PDB-8de1: TEM-1 beta-lactamase A237Y mutant covalently bound to avibactam -

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Basic information

Entry
Database: PDB / ID: 8de1
TitleTEM-1 beta-lactamase A237Y mutant covalently bound to avibactam
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE/INHIBITOR / Hydrolase / Beta-lactamase / TEM / avibactam / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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/transpeptidase-like
Similarity search - Domain/homology
Chem-NXL / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsJi, Z. / Boxer, S.G. / Mathews, I.I.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118044 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133894 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Protein Electric Fields Enable Faster and Longer-Lasting Covalent Inhibition of beta-Lactamases.
Authors: Ji, Z. / Kozuch, J. / Mathews, I.I. / Diercks, C.S. / Shamsudin, Y. / Schulz, M.A. / Boxer, S.G.
History
DepositionJun 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase TEM
B: Beta-lactamase TEM
C: Beta-lactamase TEM
D: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3138
Polymers116,2444
Non-polymers1,0694
Water22,8791270
1
A: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3282
Polymers29,0611
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3282
Polymers29,0611
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3282
Polymers29,0611
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3282
Polymers29,0611
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.610, 83.570, 95.860
Angle α, β, γ (deg.)90.000, 90.440, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 26 through 79 or resid 81...
21(chain B and (resid 26 through 79 or resid 81...
31(chain C and (resid 26 through 79 or resid 81...
41(chain D and (resid 26 through 79 or resid 81...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISALAALA(chain A and (resid 26 through 79 or resid 81...AA26 - 792 - 55
12LEULEULEULEU(chain A and (resid 26 through 79 or resid 81...AA8157
13ARGARGGLUGLU(chain A and (resid 26 through 79 or resid 81...AA83 - 11059 - 86
14HISHISARGARG(chain A and (resid 26 through 79 or resid 81...AA112 - 19188 - 167
15LEULEUTRPTRP(chain A and (resid 26 through 79 or resid 81...AA193 - 288169 - 264
16NXLNXLNXLNXL(chain A and (resid 26 through 79 or resid 81...AE301
21HISHISALAALA(chain B and (resid 26 through 79 or resid 81...BB26 - 792 - 55
22LEULEULEULEU(chain B and (resid 26 through 79 or resid 81...BB8157
23ARGARGGLUGLU(chain B and (resid 26 through 79 or resid 81...BB83 - 11059 - 86
24HISHISARGARG(chain B and (resid 26 through 79 or resid 81...BB112 - 19188 - 167
25LEULEUTRPTRP(chain B and (resid 26 through 79 or resid 81...BB193 - 288169 - 264
26NXLNXLNXLNXL(chain B and (resid 26 through 79 or resid 81...BF301
31HISHISALAALA(chain C and (resid 26 through 79 or resid 81...CC26 - 792 - 55
32LEULEULEULEU(chain C and (resid 26 through 79 or resid 81...CC8157
33ARGARGGLUGLU(chain C and (resid 26 through 79 or resid 81...CC83 - 11059 - 86
34HISHISARGARG(chain C and (resid 26 through 79 or resid 81...CC112 - 19188 - 167
35LEULEUTRPTRP(chain C and (resid 26 through 79 or resid 81...CC193 - 288169 - 264
36NXLNXLNXLNXL(chain C and (resid 26 through 79 or resid 81...CG301
41HISHISALAALA(chain D and (resid 26 through 79 or resid 81...DD26 - 792 - 55
42LEULEULEULEU(chain D and (resid 26 through 79 or resid 81...DD8157
43ARGARGGLUGLU(chain D and (resid 26 through 79 or resid 81...DD83 - 11059 - 86
44HISHISARGARG(chain D and (resid 26 through 79 or resid 81...DD112 - 19188 - 167
45LEULEUTRPTRP(chain D and (resid 26 through 79 or resid 81...DD193 - 288169 - 264
46NXLNXLNXLNXL(chain D and (resid 26 through 79 or resid 81...DH301

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Components

#1: Protein
Beta-lactamase TEM / TEM-1


Mass: 29061.053 Da / Num. of mol.: 4 / Mutation: M182T A237Y
Source method: isolated from a genetically manipulated source
Details: An extra glycine at the N-terminus / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaTEM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical
ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1270 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG3350, HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.78
ReflectionResolution: 1.56→38.3 Å / Num. obs: 135097 / % possible obs: 99.5 % / Redundancy: 13.512 % / CC1/2: 0.998 / Rmerge(I) obs: 0.201 / Rrim(I) all: 0.209 / Χ2: 0.806 / Net I/σ(I): 7.97 / Num. measured all: 1825471 / Scaling rejects: 1345
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.56-1.612.651.8291.591236431003997740.7331.90597.4
1.6-1.6413.9821.5572.05134815973496420.8111.61599.1
1.64-1.6913.8941.3632.37130967950694260.8641.41499.2
1.69-1.7413.7111.1352.78125730923491700.891.17999.3
1.74-1.813.2790.9573.28117211888588270.9240.99599.3
1.8-1.8613.0050.7543.99111826864385990.9440.78499.5
1.86-1.9313.8680.5945.07115481836183270.970.61699.6
1.93-2.0113.9850.4556.31112172804280210.9810.47299.7
2.01-2.113.7650.3857.3106003772077010.9820.499.8
2.1-2.2113.2430.2988.4997335735773500.9890.3199.9
2.21-2.3313.7560.2629.5596598702870220.9910.27299.9
2.33-2.4713.4560.22110.5789334664966390.9930.2399.8
2.47-2.6414.0280.1912.2487491623862370.9920.197100
2.64-2.8513.3250.16412.9877207579457940.9950.171100
2.85-3.1213.9390.14715.1675007538153810.9950.153100
3.12-3.4912.9330.1217.1962594484148400.9970.125100
3.49-4.0313.2490.10619.857038430743050.9970.11100
4.03-4.9313.3330.09422.2648453363736340.9980.09899.9
4.93-6.9812.750.09321.0636107283228320.9990.097100
6.98-38.312.9820.07424.8220459159015760.9990.07799.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ERM

1erm


Resolution: 1.56→38.3 Å / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 36.43 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2214 6817 5.05 %
Rwork0.2065 128350 -
obs0.2072 135091 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.48 Å2 / Biso mean: 18.8965 Å2 / Biso min: 8.83 Å2
Refinement stepCycle: final / Resolution: 1.56→38.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8132 0 68 1270 9470
Biso mean--20.52 26.98 -
Num. residues----1052
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5007X-RAY DIFFRACTION9.731TORSIONAL
12B5007X-RAY DIFFRACTION9.731TORSIONAL
13C5007X-RAY DIFFRACTION9.731TORSIONAL
14D5007X-RAY DIFFRACTION9.731TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.56-1.590.3413190.32576217653692
1.59-1.620.34123250.30876377670294
1.62-1.650.31373420.30796348669094
1.65-1.680.31123360.30776353668994
1.68-1.720.30463350.30086369670494
1.72-1.760.31363270.3056395672294
1.76-1.80.32113340.30356377671194
1.8-1.850.323400.2966415675594
1.85-1.90.33543390.29456417675695
1.9-1.970.29853420.28886395673795
1.97-2.040.32153360.28796437677395
2.04-2.120.29613320.27696407673995
2.12-2.210.27023420.27446421676395
2.21-2.330.27353380.2646486682495
2.33-2.480.25763390.2516429676895
2.48-2.670.28253390.24256456679595
2.67-2.940.24463400.23096466680695
2.94-3.360.21943480.21276504685295
3.36-4.230.20833460.18526470681695
4.23-38.30.19463420.19026611695395

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