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- PDB-3huo: X-ray crystallographic structure of CTX-M-9 S70G in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3huo
TitleX-ray crystallographic structure of CTX-M-9 S70G in complex with benzylpenicillin
ComponentsCTX-M-9 extended-spectrum beta-lactamase
KeywordsHYDROLASE / beta-lactamase / BLSE / CTX-M-9 / b-lactam / penicillin / benzylpenicillin
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-PNK / PENICILLIN G / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsDelmas, J. / Leyssene, D. / Dubois, D. / Robin, F. / Bonnet, R.
CitationJournal: To be Published
Title: Dynamic view of the early and late steps of the catalytic mechanism mediated by the emerging enzymes CTX-M.
Authors: Delmas, J. / Leyssene, D. / Dubois, D. / Birck, C. / Samama, J.-P. / Robin, F. / Bonnet, R.
History
DepositionJun 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Non-polymer description
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
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

Downloads & links

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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)57,9098
Polymers55,8852
Non-polymers2,0246
Water12,268681
1
A: CTX-M-9 extended-spectrum beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2805
Polymers27,9421
Non-polymers1,3384
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)28,6293
Polymers27,9421
Non-polymers6872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.205, 106.784, 47.645
Angle α, β, γ (deg.)90.000, 101.690, 90.000
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: pET9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE03) / References: UniProt: Q9L5C8, beta-lactamase
#2: Chemical
ChemComp-PNN / PENICILLIN G


Mass: 334.390 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H18N2O4S
#3: Chemical ChemComp-PNK / (2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / Penicillin, hydroxylated form


Mass: 352.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N2O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 2.02 Å3/Da / Density % sol: 38.96 % / Mosaicity: 0.512 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: potassium phosphate , pH 8.8, 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: Single Silicon (111)monochromator
RadiationMonochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionRedundancy: 3 % / Av σ(I) over netI: 13.09 / Rmerge(I) obs: 0.055 / Χ2: 1 / D res high: 1.35 Å / D res low: 50 Å / Num. obs: 95275 / % possible obs: 98.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.915096.410.02812.9
2.312.9199.410.05413
2.022.3199.910.05213.1
1.832.0299.910.05713.1
1.71.8399.910.07513.1
1.61.799.910.09413.1
1.521.699.910.11613.1
1.451.5299.810.1440.9993
1.41.4599.810.190.9993
1.351.490.510.24112.5
ReflectionResolution: 1.35→50 Å / Num. all: 96726 / Num. obs: 95275 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.055 / Χ2: 1 / Net I/σ(I): 13.094
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.14 / Num. unique all: 8754 / Χ2: 1 / % possible all: 90.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P74

2p74


Resolution: 1.5→34.08 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.181 3483 5 %RANDOM
Rwork0.148 ---
obs0.15 70141 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 45.51 Å2 / Biso mean: 11.403 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.126 Å
Refinement stepCycle: LAST / Resolution: 1.5→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3887 0 139 681 4707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224314
X-RAY DIFFRACTIONr_angle_refined_deg1.9892.0085929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5785582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70124.432176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61115716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1931535
X-RAY DIFFRACTIONr_chiral_restr0.0990.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023327
X-RAY DIFFRACTIONr_nbd_refined0.2760.22264
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23027
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2506
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.273
X-RAY DIFFRACTIONr_mcbond_it1.5611.52699
X-RAY DIFFRACTIONr_mcangle_it2.33124354
X-RAY DIFFRACTIONr_scbond_it2.34931615
X-RAY DIFFRACTIONr_scangle_it3.5514.51533
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 233 -
Rwork0.166 4978 -
all-5211 -
obs--99.69 %

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