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- PDB-4wz4: Crystal structure of P. aeruginosa AmpC -

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Basic information

Entry
Database: PDB / ID: 4wz4
TitleCrystal structure of P. aeruginosa AmpC
ComponentsBeta-lactamase
Keywordshydrolase/hydrolase inhibitor / beta lactamase / 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-3VU / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsFerguson, A.D.
CitationJournal: ACS Infect Dis / Year: 2015
Title: 4,5-Disubstituted 6-Aryloxy-1,3-dihydrobenzo[c][1,2]oxaboroles Are Broad-Spectrum Serine beta-Lactamase Inhibitors.
Authors: McKinney, D.C. / Zhou, F. / Eyermann, C.J. / Ferguson, A.D. / Prince, D.B. / Breen, J. / Giacobbe, R.A. / Lahiri, S. / Verheijen, J.C.
History
DepositionNov 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9273
Polymers39,5001
Non-polymers4272
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.730, 71.270, 107.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase / / Cephalosporinase


Mass: 39499.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: ampC, PA4110 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: P24735, beta-lactamase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-3VU / {(3R)-6-[(3-amino-1,2,4-thiadiazol-5-yl)oxy]-1-hydroxy-4,5-dimethyl-1,3-dihydro-2,1-benzoxaborol-3-yl}acetic acid


Mass: 335.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14BN3O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 148389 / Biso Wilson estimate: 6.69 Å2
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 1.9 / % possible all: 66.4

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→50 Å / Cor.coef. Fo:Fc: 0.9101 / Cor.coef. Fo:Fc free: 0.9403 / SU R Cruickshank DPI: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.033 / SU Rfree Blow DPI: 0.033 / SU Rfree Cruickshank DPI: 0.032
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 7454 5.02 %RANDOM
Rwork0.1866 ---
obs0.1872 148389 92.6 %-
Displacement parametersBiso mean: 11.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.4878 Å20 Å20 Å2
2---0.6268 Å20 Å2
3---0.139 Å2
Refine analyzeLuzzati coordinate error obs: 0.123 Å
Refinement stepCycle: LAST / Resolution: 1.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 29 432 3324
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012977HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.044073HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1033SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes453HARMONIC5
X-RAY DIFFRACTIONt_it2977HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.04
X-RAY DIFFRACTIONt_other_torsion15.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion368SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3912SEMIHARMONIC4
LS refinement shellResolution: 1.05→1.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2722 267 5.13 %
Rwork0.2846 4937 -
all0.284 5204 -
obs--92.6 %
Refinement TLS params.Method: refined / Origin x: -6.3023 Å / Origin y: -3.0693 Å / Origin z: 17.9207 Å
111213212223313233
T-0.041 Å2-0.0004 Å20.0003 Å2--0.0277 Å2-0.0001 Å2---0.0271 Å2
L0.1417 °20.0137 °2-0.0888 °2-0.2323 °2-0.0697 °2--0.426 °2
S-0.009 Å °-0.0218 Å °-0.0092 Å °-0.0038 Å °-0.0016 Å °-0.0023 Å °-0.001 Å °-0.0076 Å °0.0107 Å °
Refinement TLS groupSelection details: { A|* }

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