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- PDB-4xux: Structure of ampC bound to RPX-7009 at 1.75 A -

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Basic information

Entry
Database: PDB / ID: 4xux
TitleStructure of ampC bound to RPX-7009 at 1.75 A
ComponentsBeta-lactamase
KeywordsHydrolase/antibiotic / Hydrolase-antibiotic 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
Vaborbactam / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsClifton, M.C. / Abendroth, J.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Discovery of a Cyclic Boronic Acid beta-Lactamase Inhibitor (RPX7009) with Utility vs Class A Serine Carbapenemases.
Authors: Hecker, S.J. / Reddy, K.R. / Totrov, M. / Hirst, G.C. / Lomovskaya, O. / Griffith, D.C. / King, P. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Clifton, M.C. / Atkins, K. / Raymond, ...Authors: Hecker, S.J. / Reddy, K.R. / Totrov, M. / Hirst, G.C. / Lomovskaya, O. / Griffith, D.C. / King, P. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Clifton, M.C. / Atkins, K. / Raymond, A. / Potts, K.T. / Abendroth, J. / Boyer, S.H. / Loutit, J.S. / Morgan, E.E. / Durso, S. / Dudley, M.N.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.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)39,9555
Polymers39,4141
Non-polymers5414
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.560, 69.600, 76.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

21A-620-

HOH

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Components

#1: Protein Beta-lactamase / / Cephalosporinase


Mass: 39413.887 Da / Num. of mol.: 1 / Fragment: UNP residues 21-381
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: ampC / Production host: Escherichia coli (E. coli) / References: UniProt: P05364, beta-lactamase
#2: Chemical ChemComp-4D6 / Vaborbactam / {(3R,6S)-2-hydroxy-3-[(thiophen-2-ylacetyl)amino]-1,2-oxaborinan-6-yl}acetic acid / 2-((3R,6S)-2-hydroxy-3-(2-(thiophen-2-yl)acetamido)-1,2-oxaborinan-6-yl)acetic acid / 2-[(3R,6S)-2-hydroxy-3-[(2-thiophen-2-ylacetyl)amino]oxaborinan-6-yl]acetic acid / 1,2-Oxaborinane-6-acetic acid, 2-hydroxy-3-((2-(2-thienyl)acetyl)amino)-, (3R,6S)- / Vaborbactam


Mass: 297.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16BNO5S / Comment: antibiotic, inhibitor*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30mg/ml AmpC, 30% PEG3000, 0.1M TRIS, PH 7.0, 0.2M NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 13, 2011
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 0.9765
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 34340 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 20
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 4.5 / Rejects: 0 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.39 Å
Translation2.5 Å48.39 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XX2

1xx2


Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.1651 / WRfactor Rwork: 0.1379 / FOM work R set: 0.9055 / SU B: 3.358 / SU ML: 0.059 / SU R Cruickshank DPI: 0.111 / SU Rfree: 0.1039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1772 5.2 %RANDOM
Rwork0.154 34300 --
obs0.156 34340 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 37.64 Å2 / Biso mean: 9.66 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 56 407 3199
Biso mean--13.23 18.4 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022879
X-RAY DIFFRACTIONr_bond_other_d0.0010.021894
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.973940
X-RAY DIFFRACTIONr_angle_other_deg0.94134639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14624.455110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04315425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.561511
X-RAY DIFFRACTIONr_chiral_restr0.0780.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 119 -
Rwork0.203 2194 -
all-2313 -
obs--99.91 %
Refinement TLS params.Method: refined / Origin x: 10.1439 Å / Origin y: 11.5046 Å / Origin z: 18.3867 Å
111213212223313233
T0.0069 Å20.0007 Å2-0.0014 Å2-0.0021 Å2-0.0012 Å2--0.0019 Å2
L0.4444 °2-0.0435 °2-0.0174 °2-0.1984 °20.0313 °2--0.244 °2
S-0.0071 Å °-0.0191 Å °0.0174 Å °0.0076 Å °0.005 Å °-0.0048 Å °0.0122 Å °0.0152 Å °0.0021 Å °

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