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- PDB-3ixh: X-ray crystal structure of the extended-spectrum AmpC Y221G mutan... -

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Basic information

Entry
Database: PDB / ID: 3ixh
TitleX-ray crystal structure of the extended-spectrum AmpC Y221G mutant beta-lactamase in complex with cefotaxime at 2.3 Angstrom resolution
ComponentsBeta-lactamase
KeywordsHYDROLASE / serine hydrolase / beta-lactamase / cephalosporinase / extended-spectrum antibiotic resistance / Antibiotic resistance
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CEFOTAXIME, C3' cleaved, open, bound form / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsShoichet, B.K. / Thomas, V.L.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural bases for stability-function tradeoffs in antibiotic resistance.
Authors: Thomas, V.L. / McReynolds, A.C. / Shoichet, B.K.
History
DepositionSep 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Non-polymer description
Revision 2.0Sep 19, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2
Revision 2.1Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,3613
Polymers78,9642
Non-polymers3971
Water3,279182
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)39,4821
Polymers39,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8792
Polymers39,4821
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.803, 77.583, 98.887
Angle α, β, γ (deg.)90.00, 118.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 39481.801 Da / Num. of mol.: 2 / Mutation: Y221G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ampA, ampC, b4150, JW4111 / Plasmid: pOGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form


Mass: 397.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7M KPi, pH 8.7, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 26, 2009 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.3→86.822 Å / Num. all: 33810 / Num. obs: 33712 / % possible obs: 96.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.424.30.3172.32070848670.31796.2
2.42-2.574.20.2393.11947045970.23996.3
2.57-2.754.20.1933.61832243410.19396.6
2.75-2.974.20.1464.71709240800.14696.8
2.97-3.254.10.115.81543937330.1197.2
3.25-3.644.10.0926.41393333940.09297.1
3.64-4.240.0846.81197130300.08497.6
4.2-5.143.80.0817.1968825490.08197.3
5.14-7.274.30.0796.9854820010.07998
7.27-62.024.10.0825.6458911200.08297.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.44 Å59.17 Å
Translation2.44 Å59.17 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.833 / SU B: 6.829 / SU ML: 0.171 / SU R Cruickshank DPI: 0.372 / SU Rfree: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.372 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1693 5 %RANDOM
Rwork0.194 ---
all0.197 33810 --
obs0.197 33697 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.75 Å2 / Biso mean: 29.186 Å2 / Biso min: 7.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20.68 Å2
2---0.92 Å20 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 0 26 182 5792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225770
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9537884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4455714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77524.836244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71715909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9131522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214443
X-RAY DIFFRACTIONr_mcbond_it0.7111.53572
X-RAY DIFFRACTIONr_mcangle_it1.35425762
X-RAY DIFFRACTIONr_scbond_it1.95332198
X-RAY DIFFRACTIONr_scangle_it3.3044.52122
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 107 -
Rwork0.21 2350 -
all-2457 -
obs--95.9 %

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