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- PDB-4lv2: AmpC beta-lactamase in complex with [1-(6-chloropyrimidin-4-yl)-1... -

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Basic information

Entry
Database: PDB / ID: 4lv2
TitleAmpC beta-lactamase in complex with [1-(6-chloropyrimidin-4-yl)-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
Chem-N95 / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 20, 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)80,0397
Polymers79,1762
Non-polymers8635
Water7,710428
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
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1324
Polymers39,5881
Non-polymers5443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.670, 78.140, 97.250
Angle α, β, γ (deg.)90.00, 116.28, 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-N95 / [1-(6-chloropyrimidin-4-yl)-1H-pyrazol-4-yl]boronic acid


Mass: 224.412 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6BClN4O2
#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.: 428 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
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: Apr 20, 2013
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: 94603 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.77
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.65-1.690.7532.0829019677396.9
1.69-1.740.6112.7731209680199.8
1.74-1.790.4493.6630655666099.9
1.79-1.840.3384.7629595641999.9
1.84-1.910.2715.8229076630199.8
1.91-1.970.1938.0627509597499.8
1.97-2.050.14810.16270785839100
2.05-2.130.11512.8125934562199.8
2.13-2.220.09315.3224893539899.7
2.22-2.330.0811723434511199.9
2.33-2.460.06819.0322490492199.8
2.46-2.610.06121.3421322467699.8
2.61-2.790.05423.6319682435199.9
2.79-3.010.04727.0218076405599.9
3.01-3.30.04129.7816307374399.8
3.3-3.690.03832.314597341099.6
3.69-4.260.03533.8112639297299.4
4.26-5.220.03235.511595256499.7
5.22-7.380.02934.738864199199.6
7.380.02734.354213102391.2

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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: 1.65→45.578 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8553 / SU ML: 0.18 / σ(F): 1.99 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1925 3424 3.62 %
Rwork0.1723 --
obs0.173 94599 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.41 Å2 / Biso mean: 24.1658 Å2 / Biso min: 10.32 Å2
Refinement stepCycle: LAST / Resolution: 1.65→45.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5485 0 55 428 5968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135767
X-RAY DIFFRACTIONf_angle_d1.4747922
X-RAY DIFFRACTIONf_chiral_restr0.107867
X-RAY DIFFRACTIONf_plane_restr0.0081021
X-RAY DIFFRACTIONf_dihedral_angle_d13.9842052
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 (%)
1.65-1.67350.29851490.29733588373795
1.6735-1.69850.28041580.250837713929100
1.6985-1.72510.3228800.235638473927100
1.7251-1.75330.23831180.223337933911100
1.7533-1.78360.26581430.214237933936100
1.7836-1.8160.21921520.202738173969100
1.816-1.85090.19071470.237843931100
1.8509-1.88870.23071120.205138113923100
1.8887-1.92980.20461050.188438273932100
1.9298-1.97470.20151500.186838043954100
1.9747-2.02410.2161440.186238253969100
2.0241-2.07880.2141450.174938163961100
2.0788-2.140.21141590.17437703929100
2.14-2.2090.1921680.17237723940100
2.209-2.2880.19691320.170338073939100
2.288-2.37960.19871350.180238173952100
2.3796-2.48790.19711400.179238193959100
2.4879-2.6190.24051460.184138503996100
2.619-2.78310.20121590.187837723931100
2.7831-2.9980.1911720.180937693941100
2.998-3.29960.18281540.172438163970100
3.2996-3.77680.17351430.14938463989100
3.7768-4.75760.14691720.128338113983100
4.7576-45.5780.17731410.15933850399198
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)
11.24120.4171-0.15341.34880.01320.8826-0.013-0.1091-0.04060.1688-0.01440.06420.147-0.02250.02550.1786-0.00890.00540.1254-0.00960.122324.0676-9.279623.2926
21.4174-0.6146-0.41591.4818-0.43271.70820.03270.33080.2134-0.4111-0.0178-0.19980.0724-0.0124-0.00890.2477-0.02220.03430.19560.03330.203537.99713.44195.2014
31.33310.6174-0.20991.5522-0.12260.8419-0.0217-0.0713-0.02980.0581-0.0071-0.07410.05660.07120.02560.11790.012-0.00720.11120.00280.104631.9371-1.41220.3355
41.1684-0.76740.07521.59990.01861.6963-0.03280.0464-0.17890.0880.0686-0.00370.22220.2783-0.02990.16560.0132-0.02320.1772-0.00110.16278.7261-11.241623.8427
51.0578-0.2156-0.17461.3835-0.01891.0492-0.0677-0.2849-0.00370.41460.11510.1007-0.09410.0347-0.05990.2534-0.00260.02430.21050.01110.15264.533910.433836.2819
61.2454-1.014-0.12281.87930.03651.0615-0.01480.0126-0.10480.06750.03420.06420.08260.0891-0.02320.1491-0.0316-0.01190.17670.0020.162771.6795-3.071823.1799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:86)A4 - 86
2X-RAY DIFFRACTION2(chain A and resid 87:140)A87 - 140
3X-RAY DIFFRACTION3(chain A and resid 141:361)A141 - 361
4X-RAY DIFFRACTION4(chain B and resid 4:83)B4 - 83
5X-RAY DIFFRACTION5(chain B and resid 84:182)B84 - 182
6X-RAY DIFFRACTION6(chain B and resid 183:361)B183 - 361

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