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- PDB-4ev4: Crystal structure of serratia fonticola carbapenemase SFC-1 E166A... -

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Basic information

Entry
Database: PDB / ID: 4ev4
TitleCrystal structure of serratia fonticola carbapenemase SFC-1 E166A mutant with the acylenzyme intermediate of meropenem
ComponentsCarbapenem-hydrolizing beta-lactamase SFC-1
KeywordsHYDROLASE/Antibiotic / CARBAPENEMASE / HYDROLASE / ANTIBIOTIC RESISTANCE / BETA-LACTAMASE COMPLEX / 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, 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-MER / beta-lactamase
Similarity search - Component
Biological speciesSerratia fonticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFonseca, F. / Spencer, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: The basis for carbapenem hydrolysis by class A beta-lactamases: a combined investigation using crystallography and simulations.
Authors: Fonseca, F. / Chudyk, E.I. / van der Kamp, M.W. / Correia, A. / Mulholland, A.J. / Spencer, J.
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 13, 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 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Carbapenem-hydrolizing beta-lactamase SFC-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4016
Polymers30,7681
Non-polymers6345
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.185, 61.955, 79.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbapenem-hydrolizing beta-lactamase SFC-1


Mass: 30767.732 Da / Num. of mol.: 1 / Fragment: UNP residues 27-309 / Mutation: E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia fonticola (bacteria) / Strain: UTAD54 / Gene: BLASFC-1, SFC-1 / Plasmid: pET26-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6JP75, beta-lactamase
#2: Chemical ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Comment: antibiotic*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE TWO SEQADV RECORDS RELATED TO RESIDUES 255 AND 270 REPRESENT DISCREPANCIES BETWEEN THE ...THE TWO SEQADV RECORDS RELATED TO RESIDUES 255 AND 270 REPRESENT DISCREPANCIES BETWEEN THE PREVIOUSLY DEPOSITED SEQUENCE (UNP Q6JP75) AND THE EXPRESSION CLONE, ARISING EITHER FROM PCR ERRORS OR MISTAKES IN THE ORIGINAL SEQUENCE

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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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na acetate, PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2009
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 72297 / Num. obs: 68435 / % possible obs: 94.7 % / Redundancy: 11.9 % / Biso Wilson estimate: 8.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 29.7
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 5 / % possible all: 67.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4EQI

4eqi


Resolution: 1.3→37.64 Å / Num. parameters: 24459 / Num. restraintsaints: 31358 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.07%
RfactorNum. reflection% reflectionSelection details
Rfree0.155 3418 5 %RANDOM
Rwork0.114 ---
obs0.116 67206 --
all-68362 --
Refine analyzeNum. disordered residues: 32 / Occupancy sum hydrogen: 1988.05 / Occupancy sum non hydrogen: 2530.75
Refinement stepCycle: LAST / Resolution: 1.3→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 42 437 2546
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.073
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.055
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.021
X-RAY DIFFRACTIONs_approx_iso_adps0.098

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