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- PDB-3bm6: AmpC beta-lactamase in complex with a p.carboxyphenylboronic acid -

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Basic information

Entry
Database: PDB / ID: 3bm6
TitleAmpC beta-lactamase in complex with a p.carboxyphenylboronic acid
ComponentsBeta-lactamase
KeywordsHYDROLASE / AmpC / beta-lactamases / cephalosporinase / serine hydrolase / covalent inhibition / Antibiotic resistance / Periplasm
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C9P / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsTondi, D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: Structural study of phenyl boronic acid derivatives as AmpC beta-lactamase inhibitors.
Authors: Tondi, D. / Calo, S. / Shoichet, B.K. / Costi, M.P.
History
DepositionDec 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _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
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1104
Polymers79,1762
Non-polymers9352
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.908, 77.180, 97.937
Angle α, β, γ (deg.)90.00, 115.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase / / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: ampC, ampA / Plasmid: POGO295 / Production host: Escherichia Coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-C9P / 4-(dihydroxyboranyl)-2-({[4-(phenylsulfonyl)thiophen-2-yl]sulfonyl}amino)benzoic acid / 3-(4-BENZENESULFONYL-THIOPHENE-2-SULFONYLAMINO)-4-CARBOXY-PHENYLBORONIC ACID


Mass: 467.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14BNO8S3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: potassium phosphate buffer, pH 8.7, vapor diffusion, hanging drop, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorDetector: CCD / Date: Jan 12, 2005 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 3 % / Av σ(I) over netI: 19.8 / Number: 130177 / Rmerge(I) obs: 0.064 / Χ2: 1.18 / D res high: 2.1 Å / D res low: 20 Å / Num. obs: 43167 / % possible obs: 92.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.512097.610.0361.6333.1
3.594.5197.910.0461.9483.2
3.133.5998.610.061.3243.2
2.853.1398.910.0771.0333.3
2.642.8598.910.1020.9923.2
2.492.649910.1240.9343.2
2.362.4998.210.1520.8553.1
2.262.3695.110.1890.9132.7
2.172.2678.410.2320.8762.4
2.12.1762.810.2720.8872.3
ReflectionResolution: 2.1→20 Å / Num. all: 49573 / Num. obs: 46573 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.08

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementStarting model: pdb entry 1GA9

1ga9


Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2091 4.5 %RANDOM
Rwork0.201 ---
obs0.201 41919 90 %-
Solvent computationBsol: 47.82 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5532 0 60 329 5921
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3011.5
X-RAY DIFFRACTIONc_mcangle_it1.9882
X-RAY DIFFRACTIONc_scbond_it2.1862
X-RAY DIFFRACTIONc_scangle_it3.0152.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5DE29_SEBMOD.PARDE29_SEBMOD.TOP

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