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- PDB-8de2: TEM-1 beta-lactamase A237Y mutant covalently bound to avibactam, ... -

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Basic information

Entry
Database: PDB / ID: 8de2
TitleTEM-1 beta-lactamase A237Y mutant covalently bound to avibactam, a room temperature structure
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE/INHIBITOR / Hydrolase / Beta-lactamase / TEM / avibactam / room-temperature / 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: 2.45 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
Revision 1.3Oct 16, 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 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
Water1,838102
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)60.930, 86.070, 96.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: TRP / End label comp-ID: TRP / Auth seq-ID: 26 - 288 / Label seq-ID: 2 - 264

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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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*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 43.75 %
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: 297 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 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: 0.52
ReflectionResolution: 2.45→39.33 Å / Num. obs: 35092 / % possible obs: 94.9 % / Redundancy: 6.025 % / CC1/2: 0.998 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.167 / Χ2: 0.816 / Net I/σ(I): 8.54
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
2.45-2.515.8120.9781.7911648272620040.8511.07373.5
2.51-2.586.0840.8582.1514523262723870.8790.93790.9
2.58-2.666.2150.7692.4115433259924830.90.83895.5
2.66-2.746.120.622.914988247624490.9330.67798.9
2.74-2.836.1250.5413.3114718245124030.9580.59198
2.83-2.936.0870.4633.7814007235523010.9730.50697.7
2.93-3.046.0060.4214.1813442228422380.9750.4698
3.04-3.165.9120.3295.1912516215821170.9750.36198.1
3.16-3.35.7930.2486.4511111209819180.9830.27391.4
3.3-3.466.1820.1988.3312167200619680.9910.21698.1
3.46-3.656.1510.14810.3311514190218720.9940.16298.4
3.65-3.876.0480.12811.2510881182817990.9950.1498.4
3.87-4.145.9280.09114.119906169316710.9980.198.7
4.14-4.475.8290.08115.789059158415540.9970.08998.1
4.47-4.95.7570.06318.497674146313330.9990.0791.1
4.9-5.486.2020.07217.998156133413150.9990.07898.6
5.48-6.336.1710.08516.017115116411530.9980.09299.1
6.33-7.756.070.06818.3597310009840.9990.07498.4
7.75-10.965.7840.03531.741017787090.9990.03991.1
10.96-39.335.7580.02839.7824934464330.9990.03197.1

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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: 2.45→39.33 Å / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 38.09 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2495 1789 5.1 %
Rwork0.2045 33329 -
obs0.2486 35092 94.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.07 Å2 / Biso mean: 43.5318 Å2 / Biso min: 24.83 Å2
Refinement stepCycle: final / Resolution: 2.45→39.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8132 0 68 102 8302
Biso mean--40.29 39.35 -
Num. residues----1052
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5052X-RAY DIFFRACTION13.84TORSIONAL
12B5052X-RAY DIFFRACTION13.84TORSIONAL
13C5052X-RAY DIFFRACTION13.84TORSIONAL
14D5052X-RAY DIFFRACTION13.84TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.520.41941020.35121971207370
2.52-2.590.35971310.34242458258987
2.59-2.670.37391350.3432566270192
2.67-2.770.35991430.34672688283193
2.77-2.880.42781400.32942636277694
2.88-3.010.41741380.31542625276393
3.01-3.170.35351330.28982645277893
3.17-3.370.34731320.27742515264789
3.37-3.630.27271390.23172646278593
3.63-3.990.24841440.2272654279894
3.99-4.570.27651430.19812655279893
4.57-5.750.21081370.19832594273190
5.76-39.330.22071460.17552676282292

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