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- PDB-2m5d: Solution Structure of the Bacillus cereus Metallo-Beta-Lactamase ... -

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Basic information

Entry
Database: PDB / ID: 2m5d
TitleSolution Structure of the Bacillus cereus Metallo-Beta-Lactamase BcII in Complex with R-Thiomandelic Acid
ComponentsBeta-lactamase 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / BcII / Metallo-Beta-Lactamase / R-Thiomandelic Acid / mercaptocarboxylate inhibitor / broad spectrum inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
: / Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase ...: / Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(2R)-phenyl(sulfanyl)ethanoic acid / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsKarsisiotis, A.I. / Damblon, C.F. / Roberts, G.C.K.
Citation
Journal: Biochem.J. / Year: 2013
Title: Solution structures of the Bacillus cereus metallo-beta-lactamase BcII and its complex with the broad spectrum inhibitor R-thiomandelic acid.
Authors: Karsisiotis, A.I. / Damblon, C.F. / Roberts, G.C.
#1: Journal: Biomol.Nmr Assign. / Year: 2013
Title: Complete (1)H, (15)N and (13)C resonance assignments of Bacillus cereus metallo-beta-lactamase and its complex with the inhibitor R-thiomandelic acid
Authors: Karsisiotis, A.I. / Damblon, C.F. / Roberts, G.C.K.
History
DepositionFeb 20, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2954
Polymers24,9961
Non-polymers2993
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Beta-lactamase 2 / BcII / Beta-lactamase II / Cephalosporinase / Penicillinase


Mass: 24995.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: 569/H / Gene: blm / Production host: Escherichia coli (E. coli) / References: UniProt: P04190, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-RTD / (2R)-phenyl(sulfanyl)ethanoic acid / alpha-mercaptophenylacetic acid, R-thiomandelic acid


Mass: 168.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O2S

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1322D 1H-13C HSQC aliphatic
1422D 1H-13C HSQC aromatic
1523D CBCA(CO)NH
1623D HN(CA)CB
1723D HNCA
1823D HN(CA)CO
1923D HNCO
11023D (H)CCH-TOCSY
11123D (H)CCH-TOCSY
11213D 1H-15N NOESY
11323D 1H-13C NOESY aliphatic
11423D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 15N] BcII-1, 1 mM R-Thiomandelic Acid-2, 20 mM MES-3, 100 mM sodium chloride-4, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] BcII-5, 1 mM R-Thiomandelic Acid-6, 20 mM MES-7, 100 mM sodium chloride-8, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBcII-1[U-99% 15N]1
1 mMR-Thiomandelic Acid-21
20 mMMES-31
100 mMsodium chloride-41
1 mMBcII-5[U-99% 13C; U-99% 15N]2
1 mMR-Thiomandelic Acid-62
20 mMMES-72
100 mMsodium chloride-82
Sample conditionsIonic strength: 120 / pH: 6.4 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CANDIDGuntert, Mumenthaler and Wuthrichstructure solution
CANDIDGuntert, Mumenthaler and Wuthrichautomated noe assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
MOLMOLKoradi, Billeter and Wuthrichdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
XwinNMRBruker Biospincollection
ProcheckNMRLaskowski and MacArthurvalidation
WHAT IFVriendvalidation
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The refinement protocol used consisted of five cycles of simulated annealing with a high start temperature (8000 K) and a gradual slow cooling to a low temperature (100 K) in a large number ...Details: The refinement protocol used consisted of five cycles of simulated annealing with a high start temperature (8000 K) and a gradual slow cooling to a low temperature (100 K) in a large number of steps (20,000). This standard torsion angle based simulating annealing protocol with all constraints applied simultaneously is combined with cycles of redundant dihedral angle constraints (REDAC; Guntert and Wuthrich, 1991). Several cycles of this combined refinement protocol, which eliminates violations and progressively reduces target function values while improving local and overall quality, were used to generate the final converged structures. Out of an ensemble of 100 converged structures generated, the 20 best (lowest CYANA target function during refinement) structures were selected.
NMR constraintsNOE constraints total: 6578 / NOE long range total count: 2722 / NOE medium range total count: 1059 / NOE sequential total count: 2797
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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