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- PDB-4kza: Crystal structure of AmpC beta-lactamase in complex with fragment... -

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Basic information

Entry
Database: PDB / ID: 4kza
TitleCrystal structure of AmpC beta-lactamase in complex with fragment 48 (3-(cyclopropylsulfamoyl)thiophene-2-carboxylic acid)
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / AMPC beta-lactamase / class C / hydrolase / cephalosporinase / 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-NZ9 / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEidam, O. / Barelier, S. / Fish, I. / Shoichet, B.K.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Increasing chemical space coverage by combining empirical and computational fragment screens.
Authors: Barelier, S. / Eidam, O. / Fish, I. / Hollander, J. / Figaroa, F. / Nachane, R. / Irwin, J.J. / Shoichet, B.K. / Siegal, G.
History
DepositionMay 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)81,24911
Polymers79,1762
Non-polymers2,0739
Water13,926773
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9197
Polymers39,5881
Non-polymers1,3316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3304
Polymers39,5881
Non-polymers7423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.620, 76.630, 97.980
Angle α, β, γ (deg.)90.00, 116.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase / AmpC beta-lactamase / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 2 / Fragment: UNP residues 20-377
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-NZ9 / 3-(cyclopropylsulfamoyl)thiophene-2-carboxylic acid


Mass: 247.291 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H9NO4S2
#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.: 773 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
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: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2012
RadiationMonochromator: KHOZU Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.6→29.555 Å / Num. obs: 102278 / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.341 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.640.4812.4626409760399.6
1.64-1.690.3853.0725680736399.7
1.69-1.740.3163.7525047716099.8
1.74-1.790.2414.924676703199.8
1.79-1.850.1886.2823894676999.7
1.85-1.910.1687.2722591647898.2
1.91-1.980.11710.5120845613597.6
1.98-2.070.08713.5421688612099.7
2.07-2.160.06717.2820627583699.6
2.16-2.260.05919.9617656534395.4
2.26-2.390.05122.1918309524798.4
2.39-2.530.04226.4117882505099.7
2.53-2.70.03630.116751474199.5
2.7-2.920.03234.515229437899.5
2.92-3.20.02441.7813956406399.1
3.2-3.580.0249.7412649366499.2
3.58-4.130.01856.3811272320998.5
4.13-5.060.01660.610005277599.6
5.06-7.160.01658.767758214799.4
7.160.01562.424006116695.3

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Processing

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

1ke4


Resolution: 1.6→29.555 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8843 / SU ML: 0.14 / σ(F): 1.99 / Phase error: 18.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1887 3763 3.68 %
Rwork0.1598 --
obs0.1609 102263 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.61 Å2 / Biso mean: 19.6889 Å2 / Biso min: 5.54 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5529 0 125 773 6427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135902
X-RAY DIFFRACTIONf_angle_d1.5018114
X-RAY DIFFRACTIONf_chiral_restr0.104865
X-RAY DIFFRACTIONf_plane_restr0.0081046
X-RAY DIFFRACTIONf_dihedral_angle_d22.4052194
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.62020.28271500.23136193769100
1.6202-1.64150.22781540.214536793833100
1.6415-1.6640.23241500.198536133763100
1.664-1.68780.22281520.185336523804100
1.6878-1.7130.22581140.182236463760100
1.713-1.73970.1872920.176937393831100
1.7397-1.76830.2091420.179436683810100
1.7683-1.79870.21391470.165236253772100
1.7987-1.83140.19321500.171136563806100
1.8314-1.86670.21611260.1736743800100
1.8667-1.90480.2384860.19453670375698
1.9048-1.94620.26841320.22373475360795
1.9462-1.99140.18711430.159736483791100
1.9914-2.04120.19721370.150636953832100
2.0412-2.09640.16891410.151836313772100
2.0964-2.15810.18271650.148736683833100
2.1581-2.22770.19011340.15883628376298
2.2277-2.30730.20721200.18213423354393
2.3073-2.39960.19361430.151836603803100
2.3996-2.50880.21531330.157636623795100
2.5088-2.6410.20321490.15436983847100
2.641-2.80630.20141510.15573642379399
2.8063-3.02280.14951660.156936473813100
3.0228-3.32660.16821450.14543656380199
3.3266-3.80710.16811350.13683678381399
3.8071-4.79330.15451670.133537023869100
4.7933-29.56020.19721390.17173746388599
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)
11.37350.6093-0.33671.9906-0.57512.51380.1001-0.27140.07010.1992-0.07560.18330.1024-0.1782-0.02120.0972-0.06910.02810.1663-0.03340.116317.4873-10.673826.4075
21.2771-0.4011-0.30213.4383-0.41461.08150.05640.17610.11-0.2532-0.0779-0.1126-0.05380.01730.01470.0648-0.01810.00530.10570.00820.067839.2366.81998.1983
31.9810.89850.36491.3282-0.07031.18940.0754-0.22810.07980.1624-0.12270.0498-0.0148-0.05980.04510.0839-0.0290.01770.1132-0.00980.070630.2461-1.821522.7778
49.20765.18041.28427.64462.37695.53560.11250.6555-0.411-0.51830.2211-0.58330.13150.3798-0.29920.12140.09580.05780.4444-0.02580.183186.5928-12.648113.4795
50.5798-0.353-0.23591.32430.24070.6504-0.0441-0.15270.01950.14470.0982-0.03160.01790.1348-0.05130.0872-0.0486-0.01610.21070.00910.076869.05314.427233.0108
61.1032-0.79850.0421.333-0.23261.0962-0.0045-0.00330.0065-0.05440.0298-0.0670.06930.1697-0.01720.0777-0.0515-0.00710.1838-0.00060.093971.5445-3.388424.154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:66)A4 - 66
2X-RAY DIFFRACTION2(chain A and resid 67:182)A67 - 182
3X-RAY DIFFRACTION3(chain A and resid 183:361)A183 - 361
4X-RAY DIFFRACTION4(chain B and resid 4:24)B4 - 24
5X-RAY DIFFRACTION5(chain B and resid 25:172)B25 - 172
6X-RAY DIFFRACTION6(chain B and resid 173:361)B173 - 361

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