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- PDB-4lv3: AmpC beta-lactamase in complex with (3,5-di-tert-butylphenyl) bor... -

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Basic information

Entry
Database: PDB / ID: 4lv3
TitleAmpC beta-lactamase in complex with (3,5-di-tert-butylphenyl) 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
(3,5-di-tert-butylphenyl)boronic acid / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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

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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)79,7395
Polymers79,1762
Non-polymers5633
Water12,592699
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9173
Polymers39,5881
Non-polymers3292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8222
Polymers39,5881
Non-polymers2341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.550, 76.790, 98.080
Angle α, β, γ (deg.)90.000, 115.720, 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-25N / (3,5-di-tert-butylphenyl)boronic acid


Mass: 234.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H23BO2
#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.: 699 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
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: 1.42→50 Å / Num. obs: 144020 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.24 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 21.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.42-1.460.4213.47398811032493.9
1.46-1.50.3464.28404611015194.9
1.5-1.540.2655.4640049995195.2
1.54-1.590.2017.1839333966795.7
1.59-1.640.1638.638950947895.8
1.64-1.70.12810.7137693911796.5
1.7-1.760.10213.2237037888196.7
1.76-1.830.07916.735782855296.9
1.83-1.910.06819.8934087826496.9
1.91-2.010.05325.1232176782397
2.01-2.120.04229.9131193753597.6
2.12-2.250.03833.6228409707697.2
2.25-2.40.03535.8126674669197.3
2.4-2.590.02939.7825733630998.6
2.59-2.840.02742.9123549580498.5
2.84-3.180.02646.0220689527098.9
3.18-3.670.02250.1418561465798.4
3.67-4.490.01753.0516202391297.8
4.49-6.350.01652.5512524303997.3
6.350.0251.535911151986.5

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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: 1.42→44.181 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8937 / SU ML: 0.11 / σ(F): 1.99 / Phase error: 18.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1924 5499 3.82 %
Rwork0.1784 --
obs0.179 144017 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.28 Å2 / Biso mean: 26.3994 Å2 / Biso min: 16.57 Å2
Refinement stepCycle: LAST / Resolution: 1.42→44.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 39 699 6178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125718
X-RAY DIFFRACTIONf_angle_d1.4627861
X-RAY DIFFRACTIONf_chiral_restr0.091860
X-RAY DIFFRACTIONf_plane_restr0.0091012
X-RAY DIFFRACTIONf_dihedral_angle_d13.8042049
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.42-1.43610.25121840.23924403458793
1.4361-1.4530.2331860.22644463464994
1.453-1.47070.25771890.22364535472495
1.4707-1.48930.24691860.21774467465395
1.4893-1.50890.22891900.22384568475895
1.5089-1.52960.23251890.22054534472395
1.5296-1.55150.20941890.20634545473496
1.5515-1.57460.20511910.19514573476496
1.5746-1.59920.20451900.1894562475296
1.5992-1.62550.19611890.18634539472896
1.6255-1.65350.22031900.18334564475496
1.6535-1.68360.2181940.17884641483597
1.6836-1.71590.18281900.18474595478597
1.7159-1.7510.20441550.18964647480297
1.751-1.7890.19941840.17464581476597
1.789-1.83070.17091800.17314644482497
1.8307-1.87640.21351620.17734678484097
1.8764-1.92720.18461440.19124654479897
1.9272-1.98390.18521690.18634610477997
1.9839-2.04790.20121640.1824711487597
2.0479-2.12110.19961990.17644679487898
2.1211-2.2060.20182050.17744640484598
2.206-2.30640.20631510.18744644479597
2.3064-2.4280.20671800.17984714489498
2.428-2.58010.20131940.17814722491699
2.5801-2.77930.19461780.18784732491099
2.7793-3.05890.20252160.18694744496099
3.0589-3.50140.18331800.17144786496699
3.5014-4.41080.13762020.14524715491798
4.4108-44.1810.18791790.16024628480794
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)
11.10990.4708-0.12631.176-0.11460.6767-0.0136-0.1627-0.05380.1365-0.03440.06520.1717-0.02940.05060.2190.0030.01630.15490.00010.146223.9039-9.576424.1143
21.0056-0.2261-0.14911.0644-0.4041.0863-0.05340.2170.035-0.3237-0.0093-0.08130.10770.07890.05310.2416-0.00640.01550.18640.01930.159739.299413.13225.4625
31.13560.7076-0.09051.4687-0.02980.3973-0.003-0.0841-0.03290.0464-0.0353-0.07240.11820.04610.03710.16340.02390.0010.14090.00840.119832.9866-1.219620.3568
40.4668-0.4831-0.41270.88870.25290.6986-0.0308-0.0414-0.03640.01010.0388-0.01790.07880.0331-0.01010.12690.0006-0.01770.1580.00470.158478.6433-10.8724.404
50.48410.0588-0.14521.09250.38461.2947-0.0188-0.17640.06030.20570.04280.0079-0.06680.03-0.01890.19980.01330.00160.1918-0.01350.167666.009516.00336.1049
60.7278-0.4809-0.15121.0739-0.00980.84730.0083-0.0102-0.0336-0.01160.0254-0.00660.04210.0094-0.03640.1143-0.0113-0.01320.1344-0.00170.142271.4967-2.92425.8112
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 84:139)A84 - 139
3X-RAY DIFFRACTION3(chain A and resid 140:361)A140 - 361
4X-RAY DIFFRACTION4(chain B and resid 4:86)B4 - 86
5X-RAY DIFFRACTION5(chain B and resid 87:149)B87 - 149
6X-RAY DIFFRACTION6(chain B and resid 150:361)B150 - 361

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