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- PDB-5a93: 293K Joint X-ray Neutron with Cefotaxime: EXPLORING THE MECHANISM... -

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Basic information

Entry
Database: PDB / ID: 5a93
Title293K Joint X-ray Neutron with Cefotaxime: EXPLORING THE MECHANISM OF BETA-LACTAM RING PROTONATION IN THE CLASS A BETA-LACTAMASE ACYLATION MECHANISM USING NEUTRON AND X-RAY CRYSTALLOGRAPHY
ComponentsBETA-LACTAMASE CTX-M-97
KeywordsHYDROLASE / JOINT NEUTRON X-RAY / BETA LACTAMASE
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
CEFOTAXIME, C3' cleaved, open, bound form / Beta-lactamase CTX-M-97
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.598 Å
AuthorsVandavasi, V.G. / Weiss, K.L. / Cooper, J.B. / Erskine, P.T. / Tomanicek, S.J. / Ostermann, A. / Schrader, T.E. / Ginell, S.L. / Coates, L.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Exploring the Mechanism of Beta-Lactam Ring Protonation in the Class a Beta-Lactamase Acylation Mechanism Using Neutron and X-Ray Crystallography.
Authors: Vandavasi, V.G. / Weiss, K.L. / Cooper, J.B. / Erskine, P.T. / Tomanicek, S.J. / Ostermann, A. / Schrader, T.E. / Ginell, S.L. / Coates, L.
History
DepositionJul 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Jan 25, 2017Group: Data collection
Revision 1.3Feb 14, 2018Group: Data collection
Category: diffrn_detector / diffrn_radiation / diffrn_source
Item: _diffrn_detector.type / _diffrn_radiation.pdbx_diffrn_protocol ..._diffrn_detector.type / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type
Revision 1.4Jun 6, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 2.0Oct 3, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / 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 / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Nov 14, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,9957
Polymers28,1181
Non-polymers8786
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.315, 73.315, 98.870
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-2011-

HOH

21A-2215-

HOH

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Components

#1: Protein BETA-LACTAMASE CTX-M-97 / TOHO1 BETA LACTAMASE


Mass: 28117.752 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: E1ANH6, beta-lactamase
#2: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form / Cefotaxime


Mass: 397.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Comment: antibiotic*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION1

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.7354.91
22.7354.91
Crystal grow
Crystal-IDpH
15.9
26.1

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22932
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODERIGAKU FR-E DW11.541.54
NUCLEAR REACTORORNL Spallation Neutron Source MANDI233
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEApr 5, 2010
ORNL ANGER CAMERA2SNS ANGER CAMERAMIRRORS
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
231
Reflection

Entry-ID: 5A93

Resolution (Å)Num. obs% possible obs (%)Observed criterion σ(I)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)Rsym value
1.6-19.54109499.56.80.07716.1
2.2-15.211180371.403.90.17129.40.17
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.6-1.685.80.2972.8197.6
2.2-2.282.20.2523.9249.7

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Processing

Software
NameVersionClassification
CNSphasing
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
Mantiddata reduction
Mantiddata scaling
d*TREKdata reduction
d*TREKdata scaling
Refinement

% reflection Rfree: 5 % / Method to determine structure: MOLECULAR REPLACEMENT / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: PDB ENTRY 2XR0

2xr0

/ Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection obs (%)SU MLDiffraction-IDσ(F)Phase error
1.598-19.503X-RAY DIFFRACTION0.15620.13340.134520664105599.530.1211.3414.18
2.2-15.03NEUTRON DIFFRACTION0.23630.21710.2185741157972.260.2220.74
Refinement stepCycle: LAST / Resolution: 1.598→19.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 51 238 2250
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0124259
NEUTRON DIFFRACTIONf_angle_d1.2487738
NEUTRON DIFFRACTIONf_dihedral_angle_d19.2211183
NEUTRON DIFFRACTIONf_chiral_restr0.087347
NEUTRON DIFFRACTIONf_plane_restr0.007681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5981-1.63530.21981330.18812429X-RAY DIFFRACTION95
1.6353-1.67620.25291250.16682589X-RAY DIFFRACTION100
1.6762-1.72150.15641250.15822553X-RAY DIFFRACTION100
1.7215-1.77210.18991550.15382589X-RAY DIFFRACTION100
1.7721-1.82920.17481300.14412600X-RAY DIFFRACTION100
1.8292-1.89460.17061540.13462571X-RAY DIFFRACTION100
1.8946-1.97040.15051450.12762548X-RAY DIFFRACTION100
1.9704-2.05990.1551410.12542608X-RAY DIFFRACTION100
2.0599-2.16840.15441380.12282580X-RAY DIFFRACTION100
2.1684-2.30410.14031290.12042616X-RAY DIFFRACTION100
2.3041-2.48170.14751170.12612625X-RAY DIFFRACTION100
2.4817-2.73080.14351380.12422628X-RAY DIFFRACTION100
2.7308-3.12450.15861500.14132604X-RAY DIFFRACTION100
3.1245-3.93130.1351520.12522667X-RAY DIFFRACTION100
3.9313-19.50450.15391340.1322782X-RAY DIFFRACTION100
2.2001-2.42060.2537990.26282056NEUTRON DIFFRACTION55
2.4206-2.7690.28021180.23432456NEUTRON DIFFRACTION65
2.769-3.48150.24081770.22582884NEUTRON DIFFRACTION76
3.4815-15.030.2151800.19623609NEUTRON DIFFRACTION92

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