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- PDB-3hlw: CTX-M-9 S70G in complex with cefotaxime -

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Basic information

Entry
Database: PDB / ID: 3hlw
TitleCTX-M-9 S70G in complex with cefotaxime
ComponentsCTX-M-9 extended-spectrum beta-lactamase
KeywordsHYDROLASE / beta-lactamase / ESBL / CTX-M / CTX-M-9 / beta-lactam / cephalosporin / cefotaxime / michaelis / complex / Antibiotic resistance
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
Chem-CE3 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDelmas, J. / Leyssne, D. / Dubois, D. / Vazeille, E. / Robin, F. / Bonnet, R.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural insights into substrate recognition and product expulsion in CTX-M enzymes.
Authors: Delmas, J. / Leyssene, D. / Dubois, D. / Birck, C. / Vazeille, E. / Robin, F. / Bonnet, R.
History
DepositionMay 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 12, 2013Group: Non-polymer description
Revision 1.3Nov 6, 2013Group: Database references
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTX-M-9 extended-spectrum beta-lactamase
B: CTX-M-9 extended-spectrum beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7076
Polymers55,8852
Non-polymers1,8224
Water11,998666
1
A: CTX-M-9 extended-spectrum beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8533
Polymers27,9421
Non-polymers9112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CTX-M-9 extended-spectrum beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8533
Polymers27,9421
Non-polymers9112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.104, 106.564, 47.503
Angle α, β, γ (deg.)90.00, 101.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27942.467 Da / Num. of mol.: 2 / Fragment: 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: pET9 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9L5C8
#2: Chemical
ChemComp-CE3 / (6R,7R)-3-(acetyloxymethyl)-7-[[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-methoxyimino-ethanoyl]amino]-8-oxo-5-thia-1-azabicy clo[4.2.0]oct-2-ene-2-carboxylic acid / CEFOTAXIME / Cefotaxime


Mass: 455.465 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H17N5O7S2 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE NUMBERS 58, 239, 253 ARE SIMPLY SKIPPED.

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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: 38.46 %
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 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2008 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 62304 / % possible obs: 89 % / Redundancy: 3.6 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 11.5 / Num. unique all: 6928 / % possible all: 99.6

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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→5 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.087 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19855 3153 5.1 %RANDOM
Rwork0.16003 ---
obs0.16199 59132 91.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.195 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.132 Å
Refinement stepCycle: LAST / Resolution: 1.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3895 0 120 666 4681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224225
X-RAY DIFFRACTIONr_angle_refined_deg1.8921.9995784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3195558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.01224.509173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84415682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6571533
X-RAY DIFFRACTIONr_chiral_restr0.0850.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023301
X-RAY DIFFRACTIONr_nbd_refined0.2520.22266
X-RAY DIFFRACTIONr_nbtor_refined0.310.23003
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2483
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.281
X-RAY DIFFRACTIONr_mcbond_it0.9951.52684
X-RAY DIFFRACTIONr_mcangle_it1.62524313
X-RAY DIFFRACTIONr_scbond_it2.51331541
X-RAY DIFFRACTIONr_scangle_it3.8294.51446
LS refinement shellResolution: 1.5→1.535 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 246 -
Rwork0.139 4356 -
obs--97.79 %

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