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- PDB-4lv0: AmpC beta-lactamase in complex with m-aminophenyl boronic acid -

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Basic information

Entry
Database: PDB / ID: 4lv0
TitleAmpC beta-lactamase in complex with m-aminophenyl boronic acid
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / AMPC BETA-LACTAMASE / CLASS C / HYDROLASE / BORONIC ACID / COVALENT INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
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
M-AMINOPHENYLBORONIC ACID / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.652 Å
AuthorsLondon, N. / Eidam, O. / Shoichet, B.K.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Covalent docking of large libraries for the discovery of chemical probes.
Authors: London, N. / Miller, R.M. / Krishnan, S. / Uchida, K. / Irwin, J.J. / Eidam, O. / Gibold, L. / Cimermancic, P. / Bonnet, R. / Shoichet, B.K. / Taunton, J.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Nov 26, 2014Group: Database references
Revision 1.3Sep 20, 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)79,5455
Polymers79,1762
Non-polymers3693
Water14,448802
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8203
Polymers39,5881
Non-polymers2322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7252
Polymers39,5881
Non-polymers1371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.460, 77.460, 97.510
Angle α, β, γ (deg.)90.000, 116.040, 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
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-APB / M-AMINOPHENYLBORONIC ACID


Mass: 136.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8BNO2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 802 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 1.7 M POTASSIUM PHOSPHATE, pH 8.8, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2012
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 91648 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.84 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 20.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.65-1.70.5192.117029652494.1
1.7-1.740.4142.6717469658196.2
1.74-1.790.3063.6117002636896.4
1.79-1.850.2394.6116541619396.5
1.85-1.910.2085.416200606196.1
1.91-1.970.1318.7215254579295.8
1.97-2.050.09910.6715004563197.3
2.05-2.130.07414.0614632548797.7
2.13-2.230.06116.6913951523797
2.23-2.340.05320.2912602483393.9
2.34-2.460.03924.0712814481298
2.46-2.610.03228.1112093456698
2.61-2.790.02732.511319426797.8
2.79-3.020.02238.810433395097.3
3.02-3.30.01846.369581366897.6
3.3-3.690.01653.298478330096.7
3.69-4.270.01458.627498290396.9
4.27-5.220.01362.86777252698.7
5.22-7.390.01360.815223196598.8
7.390.01264.68248598487.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KE4

1ke4


Resolution: 1.652→45.672 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8643 / SU ML: 0.18 / σ(F): 1.99 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1941 3372 3.68 %
Rwork0.1639 --
obs0.165 91645 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.91 Å2 / Biso mean: 21.9469 Å2 / Biso min: 6.1 Å2
Refinement stepCycle: LAST / Resolution: 1.652→45.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5521 0 25 802 6348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145751
X-RAY DIFFRACTIONf_angle_d1.5137887
X-RAY DIFFRACTIONf_chiral_restr0.104862
X-RAY DIFFRACTIONf_plane_restr0.0081020
X-RAY DIFFRACTIONf_dihedral_angle_d13.2462043
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.652-1.67580.29671440.2553465360993
1.6758-1.70080.27591510.24223615376696
1.7008-1.72740.30041210.22323696381796
1.7274-1.75570.21621190.22193618373796
1.7557-1.7860.2651430.21723662380597
1.786-1.81850.24711400.20123680382096
1.8185-1.85340.23371470.19823656380397
1.8534-1.89130.22161120.1993711382397
1.8913-1.93240.29881060.25923597370395
1.9324-1.97730.20451370.18653694383197
1.9773-2.02680.22451320.17563698383097
2.0268-2.08160.20051400.16383719385998
2.0816-2.14280.20911610.1613691385298
2.1428-2.2120.19791650.15993701386698
2.212-2.29110.24981130.19593506361992
2.2911-2.38280.21941350.15613720385598
2.3828-2.49120.18141420.15533746388898
2.4912-2.62260.20351440.15763738388298
2.6226-2.78680.17211550.15983687384298
2.7868-3.0020.19281620.15813713387598
3.002-3.3040.17841570.1583726388398
3.304-3.78190.15351340.13813714384897
3.7819-4.7640.15721720.12613745391798
4.764-45.6720.18581400.163775391596
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)
10.90680.46490.07161.09040.1590.92790.0257-0.1468-0.04610.1883-0.06270.07560.2857-0.12420.00590.1623-0.05120.01580.0966-0.01090.103523.4166-9.520523.791
20.83790.0751-0.21571.5164-0.2391.0635-0.04160.13680.124-0.24250.0109-0.0851-0.05530.07430.01290.1382-0.03920.01160.10660.00760.119338.875110.88927.1611
31.39020.7843-0.01361.37570.09521.09190.0515-0.1465-0.00240.178-0.0712-0.04620.07790.02930.01850.1083-0.009-0.00290.07180.00220.090631.3782-2.522222.2399
40.8404-0.19230.24951.0098-0.08171.0019-0.0755-0.0196-0.15120.00430.1304-0.11560.35550.5877-0.03870.17060.07640.00380.3752-0.02150.17679.5643-10.923.7984
50.47830.0175-0.20911.34090.22321.0865-0.0126-0.12850.10480.24150.05690.0303-0.17160.0897-0.04390.1688-0.06550.00090.1677-0.01310.133463.930614.189136.8601
60.8171-0.582-0.24091.37120.08991.7516-0.0409-0.0369-0.0629-0.02280.0889-0.03670.09230.3183-0.01310.074-0.0549-0.00270.1916-0.00660.132370.9815-0.743726.266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:83)A4 - 83
2X-RAY DIFFRACTION2(chain A and resid 84:172)A84 - 172
3X-RAY DIFFRACTION3(chain A and resid 173:361)A173 - 361
4X-RAY DIFFRACTION4(chain B and resid 4:83)B4 - 83
5X-RAY DIFFRACTION5(chain B and resid 84:131)B84 - 131
6X-RAY DIFFRACTION6(chain B and resid 132:361)B132 - 361

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