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- PDB-4lv1: AmpC beta-lactamase in complex with [1-(3-chlorophenyl)-1H-pyrazo... -

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Basic information

Entry
Database: PDB / ID: 4lv1
TitleAmpC beta-lactamase in complex with [1-(3-chlorophenyl)-1H-pyrazol-4-yl] 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
[1-(3-chlorophenyl)-1H-pyrazol-4-yl]boronic acid / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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)80,0337
Polymers79,1762
Non-polymers8575
Water8,917495
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2235
Polymers39,5881
Non-polymers6354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8102
Polymers39,5881
Non-polymers2221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.580, 77.540, 97.640
Angle α, β, γ (deg.)90.00, 116.46, 90.00
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-NL9 / [1-(3-chlorophenyl)-1H-pyrazol-4-yl]boronic acid


Mass: 222.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H8BClN2O2
#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.: 495 / 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: 51.53 %
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: Sep 18, 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: 1.74→50 Å / Num. obs: 81119 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.71 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 20.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.74-1.790.5312.3721968595099.8
1.79-1.830.3993.1521605583299.8
1.83-1.890.3213.9320986567499.9
1.89-1.950.2385.3220500551099.8
1.95-2.010.1787.1919977535999.7
2.01-2.080.1399.1619223516199.7
2.08-2.160.10911.7318576496799.7
2.16-2.250.08414.8117902479099.8
2.25-2.350.07317.1117261460599.9
2.35-2.460.05820.4316543441699.7
2.46-2.590.0523.3315692418099.8
2.59-2.750.04227.3214922397599.6
2.75-2.940.03532.7713984373299.8
2.94-3.180.02939.5212902347299.6
3.18-3.480.02446.6211792319999.6
3.48-3.890.02153.2110562291299.6
3.89-4.490.01856.489036254899.1
4.49-5.50.01759.228328218999.7
5.5-7.780.01757.656441169999.4
7.780.01462.76340894998.4

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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: 1.74→45.549 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.872 / SU ML: 0.19 / σ(F): 1.99 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1953 3001 3.7 %
Rwork0.1702 --
obs0.1712 81114 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.38 Å2 / Biso mean: 20.3716 Å2 / Biso min: 6.54 Å2
Refinement stepCycle: LAST / Resolution: 1.74→45.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5502 0 55 495 6052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145784
X-RAY DIFFRACTIONf_angle_d1.4987941
X-RAY DIFFRACTIONf_chiral_restr0.107864
X-RAY DIFFRACTIONf_plane_restr0.0081025
X-RAY DIFFRACTIONf_dihedral_angle_d13.6742059
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.74-1.76850.28741410.254337053846
1.7685-1.7990.25591560.243536873843
1.799-1.83170.23611390.219937043843
1.8317-1.86690.24151370.204337143851
1.8669-1.9050.2438950.207337403835
1.905-1.94650.22641210.195937213842
1.9465-1.99170.21471530.199536943847
1.9917-2.04160.23971350.187737343869
2.0416-2.09680.21381430.172836913834
2.0968-2.15840.19661610.169636943855
2.1584-2.22810.20831450.170837283873
2.2281-2.30770.17941280.169237203848
2.3077-2.40010.22071490.176336753824
2.4001-2.50940.18781320.172737783910
2.5094-2.64170.21271410.181236863827
2.6417-2.80710.1981580.188736983856
2.8071-3.02380.20281670.184337133880
3.0238-3.32810.19111520.173137353887
3.3281-3.80940.16521400.145837283868
3.8094-4.79860.15961680.130737403908
4.7986-45.5490.18941400.156138283968
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)
11.2430.5895-0.28431.2325-0.12981.16860.0366-0.1879-0.02940.1438-0.06320.07780.2294-0.11160.02650.1471-0.0435-0.00360.0893-0.01680.096223.0039-9.509123.8817
21.7228-0.0362-0.45372.1234-0.60081.5671-0.00910.2080.1263-0.2913-0.0158-0.1291-0.06060.06350.02420.1235-0.02690.00170.10840.01370.111338.57768.57667.4239
32.17411.04820.09091.5663-0.03121.31740.0579-0.2133-0.02150.1646-0.1044-0.05730.07370.02520.03650.1045-0.0051-0.00750.06160.00540.079830.7561-1.934322.8876
41.709-0.3823-0.00471.4125-0.18931.2158-0.14350.0158-0.2783-0.05240.1284-0.19590.57630.8330.02040.24090.14980.03590.4501-0.0030.229284.1185-13.171721.6382
50.9891-0.2232-0.35171.6953-0.03381.5366-0.0278-0.20180.02790.25410.08990.0967-0.1270.1322-0.0550.1284-0.03420.00370.14760.00660.092564.23399.010735.9078
60.9516-0.8365-0.12671.7597-0.17411.8921-0.04770.0088-0.0529-0.07350.0299-0.00090.16460.29690.01290.0926-0.0324-0.00070.18030.00090.124972.4179-2.962923.4707
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 84:182)A84 - 182
3X-RAY DIFFRACTION3(CHAIN A AND RESID 183:361)A183 - 361
4X-RAY DIFFRACTION4(CHAIN B AND RESID 4:66)B4 - 66
5X-RAY DIFFRACTION5(CHAIN B AND RESID 67:182)B67 - 182
6X-RAY DIFFRACTION6(CHAIN B AND RESID 183:361)B183 - 361

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