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- PDB-3o87: Crystal structure of AmpC beta-lactamase in complex with a sulfon... -

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Basic information

Entry
Database: PDB / ID: 3o87
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
Chem-BSG / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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)79,8175
Polymers79,1762
Non-polymers6413
Water9,350519
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9563
Polymers39,5881
Non-polymers3682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8612
Polymers39,5881
Non-polymers2731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.130, 76.190, 97.380
Angle α, β, γ (deg.)90.000, 116.160, 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-BSG / 4-({[(dihydroxyboranyl)methyl]sulfamoyl}methyl)benzoic acid


Mass: 273.071 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12BNO6S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.48 Å3/Da / Density % sol: 50.48 %
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: Nov 21, 2009
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115872 Å / Relative weight: 1
ReflectionResolution: 1.78→40 Å / Num. all: 72664 / Num. obs: 72664 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 2.95 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.57
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.78-1.880.4552.73161910722195.7
1.88-2.030.2394.83753012720198
2.03-2.220.1338.23438811591198.6
2.22-2.480.09311.33179210643198.2
2.48-2.860.06515.2278649378198
2.86-3.490.04122.5229097876197.1
3.49-4.90.0328.9177296158196.9
4.9-400.02830.6106133576196.9

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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: 1.78→38.432 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8264 / SU ML: 0.21 / σ(F): 1.99 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1454 2 %Random
Rwork0.188 ---
obs0.1888 72662 97.7 %-
all-72664 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.218 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 62.66 Å2 / Biso mean: 23.1156 Å2 / Biso min: 9.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.2689 Å2-0 Å24.333 Å2
2---7.5774 Å2-0 Å2
3---6.3085 Å2
Refinement stepCycle: LAST / Resolution: 1.78→38.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5431 0 41 519 5991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115652
X-RAY DIFFRACTIONf_angle_d1.3557751
X-RAY DIFFRACTIONf_chiral_restr0.087852
X-RAY DIFFRACTIONf_plane_restr0.007995
X-RAY DIFFRACTIONf_dihedral_angle_d15.121956
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.84360.29281420.24526949709195
1.8436-1.91740.30671430.2296997714097
1.9174-2.00470.28671460.21527182732898
2.0047-2.11040.27371460.20287144729099
2.1104-2.24260.2611460.19677147729399
2.2426-2.41570.26971470.1977199734698
2.4157-2.65880.26521450.20357109725498
2.6588-3.04330.24291460.19987149729598
3.0433-3.83370.18361440.16737079722397
3.8337-38.44090.18491490.15827253740298

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