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- PDB-1dy6: Structure of the imipenem-hydrolyzing beta-lactamase SME-1 -

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Basic information

Entry
Database: PDB / ID: 1dy6
TitleStructure of the imipenem-hydrolyzing beta-lactamase SME-1
ComponentsCARBAPENEM-HYDROLYSING BETA-LACTAMASE SME-1
KeywordsHYDROLASE / LACTAMASE / ANTIBIOTIC / CARBAPENEM / IMIPENEM
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / nucleosome binding / NADP binding / oxidoreductase activity / chromatin / DNA binding
Similarity search - Function
: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / Beta-lactamase enzyme family / Beta-lactamase / DD-peptidase/beta-lactamase superfamily ...: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / Beta-lactamase enzyme family / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / NAD(P)-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsSougakoff, W. / L'Hermite, G. / Billy, I. / Guillet, V. / Naas, T. / Nordman, P. / Jarlier, V. / Delettre, J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of the Imipenem-Hydrolyzing Class a Beta-Lactamase Sme-1 from Serratia Marcescens.
Authors: Sougakoff, W. / L'Hermite, G. / Billy, I. / Pernot, L. / Guillet, V. / Naas, T. / Nordmann, P. / Jarlier, V. / Delettre, J.
#1: Journal: J.Struct.Biol. / Year: 1996
Title: Purification, Crystallization, and Preliminary X-Ray Diffraction Analysis of the Carbapenem-Hydrolyzing Class a Beta-Lactamase Sme-1 from Serratia Marcescens
Authors: Sougakoff, W. / Jarlier, V. / Delettre, J. / Colloc'H, N. / L'Hermite, G. / Nordmann, P. / Naas, T.
History
DepositionJan 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_detector / diffrn_source / Item: _diffrn_detector.detector / _diffrn_source.type
Revision 1.4Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.6Dec 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 13, 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

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Assembly

Deposited unit
A: CARBAPENEM-HYDROLYSING BETA-LACTAMASE SME-1
B: CARBAPENEM-HYDROLYSING BETA-LACTAMASE SME-1


Theoretical massNumber of molelcules
Total (without water)58,7722
Polymers58,7722
Non-polymers00
Water7,152397
1
A: CARBAPENEM-HYDROLYSING BETA-LACTAMASE SME-1


Theoretical massNumber of molelcules
Total (without water)29,3861
Polymers29,3861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CARBAPENEM-HYDROLYSING BETA-LACTAMASE SME-1


Theoretical massNumber of molelcules
Total (without water)29,3861
Polymers29,3861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.500, 51.720, 71.690
Angle α, β, γ (deg.)90.00, 118.62, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.986365, 0.004914, 0.164497), (-0.006451, 0.99994, 0.008811), (-0.164444, -0.009752, 0.986338)
Vector: -34.1322, -49.7673, -29.0392)
DetailsBIOLOGICAL UNIT: MONOMER

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Components

#1: Protein CARBAPENEM-HYDROLYSING BETA-LACTAMASE SME-1


Mass: 29386.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: APO FORM / Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: S6 / Plasmid: PPTN103 / Gene (production host): BLASME / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: Q54488, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE DESCRIBED IN NAAS T., VANDEL L., SOUGAKOFF W., LIVERMORE D.M., NORDMANN P. ANTIMICROB. ...SEQUENCE DESCRIBED IN NAAS T., VANDEL L., SOUGAKOFF W., LIVERMORE D.M., NORDMANN P. ANTIMICROB. AGENTS CHEMOTHER. 38:1262-1270(1994). NUMBERING IN THE PDB SEGMENT IS ACCORDING TO AMBLER ET AL. (BIOCHEM. J., 276 (1991) 269-272). THEREFORE, THERE ARE NO RESIDUES NUMBERED 58 AND 253, AND TWO RESIDUES HAVE BEEN ASSIGNED THE SAME NUMBER IN THE PDB ENTRY (ARG141 AND PHE141B). THE 27 FIRST RESIDUES IN THE SWS SEQUENCE ARE CLEAVED IN THE SME-1 MATURE PROTEIN. MOREOVER, NO DENSITY WAS OBSERVED FOR THE SIDE CHAINS OF THE TWO FIRST RESIDUES ASN24 AND LYS25 IN THE MATURE PROTEIN. ILE 245 WAS NOT IDENTIFIED IN THE EXPERIMENT. INSTEAD, A DENSITY FOR A TYROSINE WAS CLEARLY LOCATED, CORRESPONDING TO TYR A 241 AND TYR B 241 IN THE PDB ENTRY. THIS CORRESPONDS TO THE SWISSPROT ENTRY Q54488. THE SEQUENCE WITH ILE 245 IS GIVEN IN SWISSPROT ENTRY P52682

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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: 2.26 Å3/Da / Density % sol: 40 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 17% PEG 4000, 0.2 M AMMONIUM ACETATE, 0.1 M TRIS-HCL, PH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 %PEG40001reservoir
20.2 Mammonium acetate1reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.13→20 Å / Num. obs: 24447 / % possible obs: 82 % / Redundancy: 2.3 % / Rsym value: 0.049
Reflection
*PLUS
% possible obs: 82 % / Num. measured all: 55772 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Highest resolution: 2.13 Å / Lowest resolution: 2.28 Å / % possible obs: 30.1 % / Redundancy: 2.1 % / Num. unique obs: 1601 / Num. measured obs: 3390 / Rmerge(I) obs: 0.216

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
MADNESSdata reduction
Agrovatadata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODIFIED NMC-A BETA-LACTAMASE (1BUE) SOFTWARE USED: AMORE

1bue


Resolution: 2.13→10 Å / Rfactor Rfree error: 0.005 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
Details: A FLAT TWO-LOBE ELECTRON DENSITY IS LOCATED IN A AND IN B BETWEEN SER130, THR235 AND SER237. IT HAS BEEN ASSOCIATED WITH A MODEL OF TWO WATER MOLECULES, 111 AND 186 IN MOLECULE A AND 89 AND 143 IN MOLECULE B.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2445 10 %RANDOM
Rwork0.184 ---
obs0.184 24447 82 %-
Displacement parametersBiso mean: 19.2 Å2
Refinement stepCycle: LAST / Resolution: 2.13→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 0 397 4513
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.44
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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