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- PDB-2pu4: AmpC beta-lacamase with bound covalent oxadiazole inhibitor -

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Basic information

Entry
Database: PDB / ID: 2pu4
TitleAmpC beta-lacamase with bound covalent oxadiazole inhibitor
ComponentsBeta-lactamase
KeywordsHYDROLASE / AmpC beta-lactamase oxadiazole
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-OX6 / Chem-OX7 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBabaoglu, K. / Shoichet, B.K.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase.
Authors: Babaoglu, K. / Simeonov, A. / Irwin, J.J. / Nelson, M.E. / Feng, B. / Thomas, C.J. / Cancian, L. / Costi, M.P. / Maltby, D.A. / Jadhav, A. / Inglese, J. / Austin, C.P. / Shoichet, B.K.
History
DepositionMay 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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)80,0078
Polymers79,1762
Non-polymers8316
Water11,187621
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9073
Polymers39,5881
Non-polymers3192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0995
Polymers39,5881
Non-polymers5124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.389, 91.104, 82.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1229-

HOH

21B-1002-

HOH

Detailsbiological unit is the monomer

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Components

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Protein , 1 types, 2 molecules AB

#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) / Gene: ampC, ampA / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase

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Non-polymers , 5 types, 627 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-OX6 / TERT-BUTYL [(1R)-2-METHYL-1-(1,3,4-OXADIAZOL-2-YL)PROPYL]CARBAMATE


Mass: 241.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N3O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-OX7 / TERT-BUTYL [(1S)-2-METHYL-1-(1,3,4-OXADIAZOL-2-YL)PROPYL]CARBAMATE


Mass: 241.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N3O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 5.6 / Number: 182821 / Rmerge(I) obs: 0.126 / Χ2: 1.59 / D res high: 2 Å / D res low: 50 Å / Num. obs: 52485 / % possible obs: 92.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.315099.910.0732.5453.8
3.424.3110010.0831.9724
2.993.4299.910.121.5833.8
2.712.9998.910.1891.3133.7
2.522.7196.510.281.2723.7
2.372.529410.3421.2733.6
2.252.3792.410.3881.5063.3
2.152.2588.310.4081.2453.1
2.072.1580.410.4481.1822.9
22.077110.51.2722.5
ReflectionResolution: 2→50 Å / Num. obs: 52485 / % possible obs: 92.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.126 / Χ2: 1.585 / Net I/σ(I): 5.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.072.50.540011.272171
2.07-2.152.90.44844981.182180.4
2.15-2.253.10.40849551.245188.3
2.25-2.373.30.38851861.506192.4
2.37-2.523.60.34253131.273194
2.52-2.713.70.2854481.272196.5
2.71-2.993.70.18956321.313198.9
2.99-3.423.80.1256981.583199.9
3.42-4.3140.08357521.9721100
4.31-503.80.07360022.545199.9

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å45.88 Å
Translation2.5 Å45.88 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.87 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2642 5.1 %RANDOM
Rwork0.193 ---
obs0.195 52067 91.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.489 Å2
Baniso -1Baniso -2Baniso -3
1-2.41 Å20 Å20 Å2
2---0.7 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5600 0 52 621 6273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225808
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9567936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80524.797246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53915912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3881522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024450
X-RAY DIFFRACTIONr_nbd_refined0.210.22629
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23909
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2503
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.224
X-RAY DIFFRACTIONr_mcbond_it0.6861.53676
X-RAY DIFFRACTIONr_mcangle_it1.07825772
X-RAY DIFFRACTIONr_scbond_it1.79232529
X-RAY DIFFRACTIONr_scangle_it2.7064.52164
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 122 -
Rwork0.236 2573 -
obs-2695 65.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.59730.28240.32740.34340.17750.6456-0.039-0.05450.0222-0.0564-0.0282-0.01490.0383-0.04440.0672-0.00050.00530.0172-0.05290.0009-0.051134.6431-2.6715-8.9287
20.2376-0.1371-0.2580.47460.19490.82580.02110.0151-0.00750.0288-0.042-0.0252-0.0131-0.00630.0209-0.0074-0.0071-0.0093-0.03760.0057-0.047235.38932.9269-32.5586
30.03590.0050.00350.041-0.02010.0564-0.01580.00360.0016-0.0042-0.008-0.0122-0.0036-0.01570.02370.02980.00010.00360.01730.00270.021234.681514.467-20.2761
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 361
2X-RAY DIFFRACTION2B4 - 361
3X-RAY DIFFRACTION3A803
4X-RAY DIFFRACTION3B701 - 804
5X-RAY DIFFRACTION3A902 - 1235
6X-RAY DIFFRACTION3B903 - 1189

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