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- PDB-7ti1: Structure of AmpC bound to RPX-7063 at 2.0A -

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Basic information

Entry
Database: PDB / ID: 7ti1
TitleStructure of AmpC bound to RPX-7063 at 2.0A
ComponentsBeta-lactamase
KeywordsHYDROLASE / AmpC / 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/transpeptidase-like
Similarity search - Domain/homology
Chem-ZXQ / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsClifton, M.C. / Abendroth, J. / Edwards, T.E. / Hecker, S.J.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Bioorg.Med.Chem. / Year: 2022
Title: Broad-spectrum cyclic boronate beta-lactamase inhibitors featuring an intramolecular prodrug for oral bioavailability.
Authors: Raja Reddy, K. / Totrov, M. / Lomovskaya, O. / Griffith, D.C. / Tarazi, Z. / Clifton, M.C. / Hecker, S.J.
History
DepositionJan 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0495
Polymers41,5811
Non-polymers4694
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.960, 77.980, 62.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 41580.684 Da / Num. of mol.: 1
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-ZXQ / {(3R,7S)-2-hydroxy-3-[2-(thiophen-2-yl)acetamido]-2,3,4,7-tetrahydro-1,2-oxaborepin-7-yl}acetic acid


Mass: 309.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16BNO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 30% PEG3000, 0.1M Tris pH 7.0, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 28, 2011 / Details: Rigaku VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 23033 / % possible obs: 98.7 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 21.324 Å2 / Rmerge(I) obs: 0.096 / Net I/av σ(I): 16.34 / Net I/σ(I): 16.34
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
2-2.054.130.3514.71489187.8
2.05-2.114.90.2926.31572195.9
2.11-2.176.320.2787.71633199.9
2.17-2.247.060.2469.21544199.9
2.24-2.317.050.2289.81518199.9
2.31-2.397.130.20110.614711100
2.39-2.487.120.17611.61419199.8
2.48-2.587.180.15612.613871100
2.58-2.77.150.1421313081100
2.7-2.837.180.12414.11246199.9
2.83-2.987.210.0981612151100
2.98-3.167.20.08118.111331100
3.16-3.387.230.06722.610781100
3.38-3.657.190.05230.710071100
3.65-47.120.04835.8929199.8
4-4.477.040.04836.7847199.6
4.47-5.167.030.0534.67591100
5.16-6.326.980.05828.5653199.8
6.32-8.946.80.0530.65161100
8.94-506.050.03244309198.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1xx2

1xx2


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.547 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1184 5.1 %RANDOM
Rwork0.16 21849 --
obs0.163 23033 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.5 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2741 0 30 328 3099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022885
X-RAY DIFFRACTIONr_bond_other_d0.0010.021893
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9613954
X-RAY DIFFRACTIONr_angle_other_deg0.94334649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77724.741116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21315441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8911511
X-RAY DIFFRACTIONr_chiral_restr0.1150.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02563
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 73 -
Rwork0.19 1308 -
all-1381 -
obs--87.02 %
Refinement TLS params.Method: refined / Origin x: 58.095 Å / Origin y: 18.9947 Å / Origin z: 52.0762 Å
111213212223313233
T0.0109 Å20.0041 Å20.0051 Å2-0.0021 Å20.0045 Å2--0.0218 Å2
L0.2622 °2-0.0661 °2-0.0816 °2-0.0962 °20.0316 °2--0.4378 °2
S0.0393 Å °0.0136 Å °0.0157 Å °-0.016 Å °-0.0071 Å °-0.0031 Å °-0.0256 Å °-0.0058 Å °-0.0322 Å °

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