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- PDB-3bfc: class A beta-lactamase SED-G238C complexed with imipenem -

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Basic information

Entry
Database: PDB / ID: 3bfc
Titleclass A beta-lactamase SED-G238C complexed with imipenem
ComponentsClass A beta-lactamase Sed1
KeywordsHYDROLASE / BETA-LACTAMASE / CLASS A / SED-G238C / IMIPENEM / ACYL-ENZYME
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-IM2 / Beta-lactamase
Similarity search - Component
Biological speciesCitrobacter sedlakii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPernot, L. / Petrella, S. / Sougakoff, W.
Citation
Journal: To be Published
Title: Acyl-intermediate structures of the class A beta-lactamase SED-G238C
Authors: Pernot, L. / Petrella, S. / Sougakoff, W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary X-ray diffraction study of the class A beta-lactamase SED-1 and its mutant SED-G238C from Citrobacter sedlakii
Authors: Petrella, S. / Pernot, L. / Sougakoff, W.
History
DepositionNov 21, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Non-polymer description
Revision 1.3Nov 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 / 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class A beta-lactamase Sed1
B: Class A beta-lactamase Sed1
C: Class A beta-lactamase Sed1
D: Class A beta-lactamase Sed1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5268
Polymers113,3214
Non-polymers1,2054
Water11,169620
1
A: Class A beta-lactamase Sed1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6322
Polymers28,3301
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Class A beta-lactamase Sed1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6322
Polymers28,3301
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Class A beta-lactamase Sed1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6322
Polymers28,3301
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Class A beta-lactamase Sed1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6322
Polymers28,3301
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)188.436, 73.399, 105.050
Angle α, β, γ (deg.)90.00, 122.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Class A beta-lactamase Sed1


Mass: 28330.221 Da / Num. of mol.: 4 / Fragment: SED-G238C, UNP residues 34-295 / Mutation: G238C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter sedlakii (bacteria) / Strain: 2596 / Gene: bla-SED-1 / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q93PQ0, beta-lactamase
#2: Chemical
ChemComp-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS COORDINATES IS USED NON-SEQUENTIAL RESIDUE NUMBERING. THREE NUMBERS, 58, 239, AND 253 WERE ...THIS COORDINATES IS USED NON-SEQUENTIAL RESIDUE NUMBERING. THREE NUMBERS, 58, 239, AND 253 WERE SIMPLY SKIPPED IN THE NUMBERING AND HAVE NOTHING TO DO WITH LACK OF ELECTRON DENSITY.

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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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 35% PEG MME 2000, 200mM KSCN, 100mM SODIUM CACODYLATE pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.984 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 16, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. all: 60669 / Num. obs: 60669 / % possible obs: 98.4 % / Redundancy: 3.9 % / Rsym value: 0.117 / Net I/σ(I): 8.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.87 / Num. unique all: 8049 / Rsym value: 0.291 / % possible all: 90.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
MOLREPphasing
CNS1.1refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BFD

3bfd


Resolution: 2.2→35 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3061 -RANDOM
Rwork0.206 ---
obs0.215 57592 98.2 %-
all-60653 --
Displacement parametersBiso mean: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.21 Å20 Å2-2.44 Å2
2---3.28 Å20 Å2
3---7.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7948 0 80 620 8648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.282 473 -
Rwork0.252 9238 -
obs-9238 90.6 %

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