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- PDB-3o86: Crystal structure of AmpC beta-lactamase in complex with a sulfon... -

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Basic information

Entry
Database: PDB / ID: 3o86
TitleCrystal structure of AmpC beta-lactamase in complex with a sulfonamide boronic acid inhibitor
ComponentsBeta-lactamase
KeywordsHYDROLASE / Contains alpha helices and a beta sandwich / Beta-lactamase-like fold / AMPC beta-Lactamase / class C / cephalosporinase
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
{[(benzylsulfonyl)amino]methyl}boronic acid / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEidam, O. / Romagnoli, C. / Karpiak, J. / Shoichet, B.K.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Design, Synthesis, Crystal Structures, and Antimicrobial Activity of Sulfonamide Boronic Acids as beta-Lactamase Inhibitors
Authors: Eidam, O. / Romagnoli, C. / Caselli, E. / Babaoglu, K. / Pohlhaus, D.T. / Karpiak, J. / Bonnet, R. / Shoichet, B.K. / Prati, F.
History
DepositionAug 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...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 / 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8246
Polymers79,1762
Non-polymers6484
Water14,754819
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9123
Polymers39,5881
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9123
Polymers39,5881
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.340, 76.880, 97.760
Angle α, β, γ (deg.)90.000, 116.110, 90.000
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 / Fragment: Beta-lactamase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ampA, ampC, b4150, JW4111 / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-BSF / {[(benzylsulfonyl)amino]methyl}boronic acid


Mass: 229.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12BNO4S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 819 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7 M Potassium Phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2010
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115872 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 102737 / Num. obs: 102737 / % possible obs: 99 % / Observed criterion σ(F): 1.99 / Observed criterion σ(I): -3 / Redundancy: 3.85 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.42
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.690.443.15859515381198.6
1.69-1.790.27355398413845199.7
1.79-1.910.177.85112613068199.6
1.91-2.070.10112.65081312989199.5
2.07-2.260.06618.44281110982199
2.26-2.530.05222.64050610456199
2.53-2.920.04127.4347549083198.9
2.92-3.580.03234290217773198.7
3.58-5.10.02738.5227086057198.6
5.1-300.02238.8115553103193.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHENIX1.6_289phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KE4

1ke4


Resolution: 1.6→29.584 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.8805 / SU ML: 0.18 / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3002 2.92 %Random
Rwork0.1669 ---
obs0.1676 102732 99.12 %-
all-102737 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.047 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 66.64 Å2 / Biso mean: 22.658 Å2 / Biso min: 8.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.128 Å2-0 Å24.4057 Å2
2---0.4702 Å2-0 Å2
3---0.5982 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5448 0 40 819 6307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015761
X-RAY DIFFRACTIONf_angle_d1.3237919
X-RAY DIFFRACTIONf_chiral_restr0.09875
X-RAY DIFFRACTIONf_plane_restr0.0071014
X-RAY DIFFRACTIONf_dihedral_angle_d14.5542037
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.62630.29631410.2564555469696
1.6263-1.65430.25551470.226847584905100
1.6543-1.68440.23221480.207147744922100
1.6844-1.71680.23981470.202847764923100
1.7168-1.75180.23451480.192647674915100
1.7518-1.78990.23681450.185947084853100
1.7899-1.83150.21491480.177847874935100
1.8315-1.87730.19491480.17247714919100
1.8773-1.92810.19781460.172347394885100
1.9281-1.98480.22951290.1747694898100
1.9848-2.04880.19391340.172147544888100
2.0488-2.1220.24331370.16644799493699
2.122-2.2070.19211450.16744757490299
2.207-2.30740.18881360.16144709484599
2.3074-2.4290.19841460.1694788493499
2.429-2.58110.2181420.1724727486999
2.5811-2.78020.19881440.17614756490099
2.7802-3.05980.18961380.17214777491599
3.0598-3.50190.16081440.15554771491599
3.5019-4.40970.14561460.12944777492399
4.4097-29.58870.17071430.15194711485496

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