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- PDB-5g18: Direct Observation of Active-site Protonation States in a Class A... -

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Basic information

Entry
Database: PDB / ID: 5g18
TitleDirect Observation of Active-site Protonation States in a Class A beta lactamase with a monobactam substrate
ComponentsBETA-LACTAMASE CTX-M-97
KeywordsHYDROLASE / BETA LACTAMASE / TOHO / NEUTRON
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AZR / Beta-lactamase CTX-M-97 / Beta-lactamase Toho-1
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.1 Å
AuthorsVandavasi, V.G. / Weiss, K.L. / Parks, J.M. / Cooper, J.B. / Ginell, S.L. / Coates, L.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: Active-Site Protonation States in an Acyl-Enzyme Intermediate of a Class A beta-Lactamase with a Monobactam Substrate.
Authors: Vandavasi, V.G. / Langan, P.S. / Weiss, K.L. / Parks, J.M. / Cooper, J.B. / Ginell, S.L. / Coates, L.
History
DepositionMar 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 2.0Oct 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE CTX-M-97
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0367
Polymers28,1181
Non-polymers9186
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.445, 72.445, 97.611
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2047-

HOH

21A-2475-

HOH

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Components

#1: Protein BETA-LACTAMASE CTX-M-97 / TOH0-1 BETA LACTAMASE


Mass: 28117.752 Da / Num. of mol.: 1 / Fragment: RESIDUES 30-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: E1ANH6, UniProt: Q47066*PLUS, beta-lactamase
#2: Chemical ChemComp-AZR / 2-({[(1Z)-1-(2-amino-1,3-thiazol-4-yl)-2-oxo-2-{[(2S,3S)-1-oxo-3-(sulfoamino)butan-2-yl]amino}ethylidene]amino}oxy)-2-methylpropanoic acid / AZTREONAM, open form


Mass: 437.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N5O8S2 / Comment: antibiotic*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsAZTREONAM (AZR): BOUND TO SER 70

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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: 2.63 Å3/Da / Density % sol: 53.23 % / Description: NONE
Crystal growpH: 6.1 / Details: pH 6.1

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Data collection

DiffractionMean temperature: 15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.1→32.5 Å / Num. obs: 113081 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 6.71 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.3
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.1→32.537 Å / SU ML: 0.07 / σ(F): 1.34 / Phase error: 10.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1405 5687 5 %
Rwork0.1242 --
obs0.125 113081 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→32.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 53 506 2525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072123
X-RAY DIFFRACTIONf_angle_d1.1722912
X-RAY DIFFRACTIONf_dihedral_angle_d22.449790
X-RAY DIFFRACTIONf_chiral_restr0.075340
X-RAY DIFFRACTIONf_plane_restr0.008377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11250.16081810.14883659X-RAY DIFFRACTION96
1.1125-1.12560.17382020.1473613X-RAY DIFFRACTION96
1.1256-1.13930.16771710.143590X-RAY DIFFRACTION95
1.1393-1.15380.17292050.13563566X-RAY DIFFRACTION95
1.1538-1.16890.15541810.13393657X-RAY DIFFRACTION95
1.1689-1.18490.16831970.13183539X-RAY DIFFRACTION95
1.1849-1.20190.15891790.13133598X-RAY DIFFRACTION95
1.2019-1.21980.15951920.12483585X-RAY DIFFRACTION95
1.2198-1.23890.13851840.12353594X-RAY DIFFRACTION95
1.2389-1.25920.12812160.12583542X-RAY DIFFRACTION95
1.2592-1.28090.14611800.12383607X-RAY DIFFRACTION95
1.2809-1.30420.13722030.1163570X-RAY DIFFRACTION95
1.3042-1.32930.13841870.11823534X-RAY DIFFRACTION94
1.3293-1.35640.12441830.11953583X-RAY DIFFRACTION95
1.3564-1.38590.13921900.11533600X-RAY DIFFRACTION94
1.3859-1.41810.13432150.11333585X-RAY DIFFRACTION94
1.4181-1.45360.15071840.11253579X-RAY DIFFRACTION95
1.4536-1.49290.11252040.10643566X-RAY DIFFRACTION95
1.4929-1.53680.13022000.11043584X-RAY DIFFRACTION94
1.5368-1.58640.12071830.10843564X-RAY DIFFRACTION95
1.5864-1.64310.13211820.11023594X-RAY DIFFRACTION94
1.6431-1.70890.13611820.11243630X-RAY DIFFRACTION95
1.7089-1.78670.12982010.11673573X-RAY DIFFRACTION94
1.7867-1.88090.12691790.11643588X-RAY DIFFRACTION94
1.8809-1.99870.12931790.11813609X-RAY DIFFRACTION94
1.9987-2.1530.13451920.11223571X-RAY DIFFRACTION93
2.153-2.36960.11932060.11643569X-RAY DIFFRACTION93
2.3696-2.71240.13781840.1253581X-RAY DIFFRACTION92
2.7124-3.41670.14681680.13463570X-RAY DIFFRACTION91
3.4167-32.55120.16611770.15023394X-RAY DIFFRACTION83

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