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- PDB-6unb: Crystal structure of CTX-M-14 in complex with temocillin -

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Basic information

Entry
Database: PDB / ID: 6unb
TitleCrystal structure of CTX-M-14 in complex with temocillin
ComponentsBeta-lactamase
KeywordsHYDROLASE / temocillin / ticarcillin / b-lactam / lactam / penicillin / CTX-M-14 beta-lactamase / ESBL / extended spectrum b-lactamase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Chem-TJ7 / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSacco, M. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI147654 United States
CitationJournal: Antimicrob.Agents Chemother. / Year: 2019
Title: Influence of the alpha-Methoxy Group on the Reaction of Temocillin with Pseudomonas aeruginosa PBP3 and CTX-M-14 beta-Lactamase.
Authors: Sacco, M.D. / Kroeck, K.G. / Kemp, M.T. / Zhang, X. / Andrews, L.D. / Chen, Y.
History
DepositionOct 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Dec 18, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 2.1Dec 25, 2019Group: Database references / Category: struct_ref_seq_dif
Revision 2.2Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 2.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1808
Polymers55,9672
Non-polymers1,2136
Water13,187732
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)45.110, 106.460, 47.670
Angle α, β, γ (deg.)90.000, 101.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 27983.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-14 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2S1PK93, UniProt: Q9L5C7*PLUS, beta-lactamase
#2: Chemical ChemComp-TJ7 / (2R,4S)-2-[(1S)-1-{[(2R)-2-carboxy-2-(thiophen-3-yl)acetyl]amino}-1-methoxy-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4 -carboxylic acid / temocillin


Mass: 416.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N2O7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.2 M potassium phosphate pH 8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.296→53.23 Å / Num. all: 108653 / Num. obs: 108653 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.095 / Rsym value: 0.081 / Net I/av σ(I): 7.8 / Net I/σ(I): 10 / Num. measured all: 402420
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.3-1.373.60.5811.356139157700.3620.6870.581299.2
1.37-1.453.60.4221.854463149520.260.4970.4222.8100
1.45-1.553.70.2892.651849141160.1770.340.2894.1100
1.55-1.673.70.2023.748671131370.1220.2370.2025.8100
1.67-1.833.70.1335.645080120820.080.1560.1338.2100
1.83-2.053.80.0858.441051109260.0510.0990.08512.7100
2.05-2.373.80.06410.53655596550.0380.0750.06417.5100
2.37-2.93.80.051133107481600.030.0590.05121.6100
2.9-4.13.80.03617.42423563390.0210.0420.03629.4100
4.1-46.6423.80.02820.71330335160.0160.0320.02830.6100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ua6

4ua6


Resolution: 1.3→46.69 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.893 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1671 5540 5.1 %RANDOM
Rwork0.1247 ---
obs0.1268 103064 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 154.58 Å2 / Biso mean: 11.249 Å2 / Biso min: 4 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0.37 Å2
2--0.33 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.3→46.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3907 0 74 754 4735
Biso mean--18.22 25.87 -
Num. residues----523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134166
X-RAY DIFFRACTIONr_bond_other_d0.0090.0173897
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.6725691
X-RAY DIFFRACTIONr_angle_other_deg1.5911.5859033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5425543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07322.129202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78715681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2491532
X-RAY DIFFRACTIONr_chiral_restr0.0750.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024742
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02814
X-RAY DIFFRACTIONr_rigid_bond_restr6.97638063
LS refinement shellResolution: 1.3→1.33 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.267 446 -
Rwork0.248 7489 -
obs--98.4 %

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