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- PDB-6i30: Crystal structure of the AmpC from Pseudomonas aeruginosa with 1C -

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Basic information

Entry
Database: PDB / ID: 6i30
TitleCrystal structure of the AmpC from Pseudomonas aeruginosa with 1C
ComponentsClass C beta-lactamase PDC-301
KeywordsHYDROLASE / cyclic boronates / antimicrobial resistance / beta-lactamase / ANTIBIOTIC
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-C6S / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 Å
AuthorsBrem, J. / Cahill, S.T. / McDonough, M.A. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2019
Title: Studies on the inhibition of AmpC and other beta-lactamases by cyclic boronates.
Authors: Cahill, S.T. / Tyrrell, J.M. / Navratilova, I.H. / Calvopina, K. / Robinson, S.W. / Lohans, C.T. / McDonough, M.A. / Cain, R. / Fishwick, C.W.G. / Avison, M.B. / Walsh, T.R. / Schofield, C.J. / Brem, J.
History
DepositionNov 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class C beta-lactamase PDC-301
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6162
Polymers39,2991
Non-polymers3171
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.040, 75.340, 100.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Class C beta-lactamase PDC-301


Mass: 39299.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaPDC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Z4BUZ1
#2: Chemical ChemComp-C6S / (3R)-3-(cyclohexylcarbonylamino)-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid


Mass: 317.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20BNO5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Zinc acetate dihydrate, 0.1 M Imidazole pH = 8.0 20 % w/v PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2016 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.21→21.962 Å / Num. obs: 17758 / % possible obs: 99.8 % / Redundancy: 6.99 % / Biso Wilson estimate: 26.25 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.183 / Rrim(I) all: 0.197 / Χ2: 0.899 / Net I/σ(I): 9.39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.21-2.276.9810.7742.6424760.3940.836100
2.27-2.337.1270.7342.8923920.4830.792100
2.33-2.47.1130.623.3523200.620.669100
2.4-2.477.0140.6383.1922360.620.689100
2.47-2.556.760.5973.4322030.7070.64799.9
2.55-2.646.8410.5233.9720940.7950.566100
2.64-2.747.1450.4474.6620670.8560.482100
2.74-2.856.9560.3915.3419840.8940.423100
2.85-2.986.8450.346.1618790.9410.368100
2.98-3.137.2540.2897.3917800.9590.31199.9
3.13-3.297.2010.2328.9817180.9750.25100
3.29-3.496.9530.1711.6516410.9870.183100
3.49-3.746.6120.12714.7214960.9910.13899.3
3.74-4.047.0590.09918.7214250.9950.106100
4.04-4.426.70.07821.5912950.9970.08599.8
4.42-4.947.1280.06726.1111830.9970.073100
4.94-5.717.1350.06524.0810300.9980.07100
5.71-6.996.80.07421.798930.9970.0899.9
6.99-9.887.0430.04332.46740.9990.04699.7
9.88-21.9627.1890.03239.123490.9990.03490.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wyy

4wyy


Resolution: 2.21→21.962 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.87
RfactorNum. reflection% reflection
Rfree0.256 894 5.03 %
Rwork0.2211 --
obs0.2229 17758 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.78 Å2 / Biso mean: 36.1068 Å2 / Biso min: 10.64 Å2
Refinement stepCycle: final / Resolution: 2.21→21.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 23 89 2737
Biso mean--25.06 29.15 -
Num. residues----358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032738
X-RAY DIFFRACTIONf_angle_d0.5883749
X-RAY DIFFRACTIONf_chiral_restr0.041410
X-RAY DIFFRACTIONf_plane_restr0.004494
X-RAY DIFFRACTIONf_dihedral_angle_d10.2361609
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2101-2.34840.3141330.299627722905
2.3484-2.52950.34981560.279127632919
2.5295-2.78360.30241440.259527672911
2.7836-3.18530.26341550.22627812936
3.1853-4.00920.22351310.190628392970
4.0092-21.9630.21891750.187329423117
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)
10.64290.14150.28530.15790.26440.44980.0048-0.4862-0.07160.13770.005-0.05220.04560.0151-0.40440.29760.0171-0.04731.21-0.23330.21195.37784.56884.0732
23.89420.00860.18431.0305-0.28091.84080.09110.0491-0.1363-0.15250.0284-0.03490.0257-0.1983-0.08990.20910.0164-0.00930.1382-0.03860.1802-8.87116.437-24.0649
32.8674-0.33110.53411.5166-0.29041.9170.1089-0.9428-0.222-0.0124-0.09610.2751-0.0401-0.0113-0.01080.1957-0.07160.02210.3567-0.02240.2374-16.27466.9345-12.7542
42.65451.7949-0.68732.24710.40520.97220.1863-0.3903-0.77830.00130.0426-0.05420.21290.1206-0.17290.26640.0047-0.09090.06910.03450.51820.8983-3.7909-17.7715
50.72220.635-0.42420.72080.00631.38260.1237-0.1316-0.2448-0.07450.0484-0.04370.07520.4337-0.09840.29010.0566-0.0450.1487-0.1590.35534.39853.5628-21.4202
64.04591.2493-0.72434.99932.46664.37240.1894-0.9618-0.075-0.0139-0.0073-0.33680.18010.0872-0.16330.1825-0.0376-0.02950.3238-0.01010.15273.56433.578-7.5133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 49 )A30 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 193 )A50 - 193
3X-RAY DIFFRACTION3chain 'A' and (resid 194 through 254 )A194 - 254
4X-RAY DIFFRACTION4chain 'A' and (resid 255 through 314 )A255 - 314
5X-RAY DIFFRACTION5chain 'A' and (resid 315 through 349 )A315 - 349
6X-RAY DIFFRACTION6chain 'A' and (resid 350 through 387 )A350 - 387

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