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- PDB-3q07: CTX-M-9 S70G in complex with piperacillin -

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Basic information

Entry
Database: PDB / ID: 3q07
TitleCTX-M-9 S70G in complex with piperacillin
ComponentsBeta-lactamase
KeywordsHydrolase/Antibiotic / beta-lactamase / ESBL / CTX-M / CTX-M-9 / beta-lactam / piperacillin / michaelis / Antibiotic resistance / Hydrolase / alpha beta fold / Hydrolase-Antibiotic complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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
Piperacillin / Hydrolyzed piperacillin / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDelmas, J. / Leyssne, D. / Robin, F. / Coignoux, A. / Bonnet, R.
CitationJournal: To be Published
Title: CTX-M-9 S70G mutant in complex with piperacillin
Authors: Leyssne, D. / Delmas, J. / Coignoux, A. / Robin, F. / Bonnet, R.
History
DepositionDec 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,5277
Polymers55,8852
Non-polymers2,6425
Water14,178787
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9963
Polymers27,9421
Non-polymers1,0532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5314
Polymers27,9421
Non-polymers1,5893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.128, 106.340, 47.610
Angle α, β, γ (deg.)90.00, 101.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase / Beta-lactamase CTX-M / Beta-lactamase CTX-M-9a / Betalactamase CTX-M-9 / CTX-M-9 beta-lactamase / ...Beta-lactamase CTX-M / Beta-lactamase CTX-M-9a / Betalactamase CTX-M-9 / CTX-M-9 beta-lactamase / CTX-M-9 extended-spectrum beta-lactamase


Mass: 27942.467 Da / Num. of mol.: 2
Fragment: extended-spectrum beta-lactamase, UNP residues 29-291
Mutation: S70G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-9, blaCTX-M-9a, blaCTX-M-9b / Plasmid: pET-9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9L5C8, beta-lactamase
#2: Chemical ChemComp-WPP / Piperacillin / (2S,5R,6R)-6-{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}-3,3-dimethyl-7-oxo-4-thi a-1-azabicyclo[3.2.0]heptane-2-carboxylic acid


Mass: 517.555 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27N5O7S / Comment: antibiotic*YM
#3: Chemical ChemComp-YPP / Hydrolyzed piperacillin / (2R,4S)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid


Mass: 535.570 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H29N5O8S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / 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 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.8M phosphate , pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2008 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 100755 / % possible obs: 93.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.6
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 5.9 / Num. unique all: 9657 / % possible all: 90.1

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P74

2p74


Resolution: 1.5→19.65 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17519 3328 5 %RANDOM
Rwork0.1457 ---
obs0.14719 62848 94.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.853 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3891 0 183 787 4861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224347
X-RAY DIFFRACTIONr_angle_refined_deg1.632.0115998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8735590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.0524.706170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25515707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0121531
X-RAY DIFFRACTIONr_chiral_restr0.1110.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.024084
X-RAY DIFFRACTIONr_nbd_refined0.2880.32362
X-RAY DIFFRACTIONr_nbtor_refined0.3230.53127
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.51083
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.3100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.5162
X-RAY DIFFRACTIONr_mcbond_it1.74322738
X-RAY DIFFRACTIONr_mcangle_it2.53834445
X-RAY DIFFRACTIONr_scbond_it2.88221609
X-RAY DIFFRACTIONr_scangle_it4.31931515
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 246 -
Rwork0.134 4652 -
obs--95.11 %

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