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- PDB-1o7e: Crystal structure of the class A beta-lactamse L2 from Stenotroph... -

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Basic information

Entry
Database: PDB / ID: 1o7e
TitleCrystal structure of the class A beta-lactamse L2 from Stenotrophomonas maltophilia at 1.51 angstrom
ComponentsL2 BETA LACTAMASE
KeywordsHYDROLASE / BETA-LACTAMASE / CLASS A / L2
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Beta-lactamase / DD-peptidase/beta-lactamase superfamily ...: / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSTENOTROPHOMONAS MALTOPHILIA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsPernot, L. / Petrella, S. / Sougakoff, W.
CitationJournal: To be Published
Title: Role of the Disulfide Bridge Cys69-Cys238 in Class a B-Lactamases : A Structural and Biochemical Investigation on the B-Lactamase L2 from Stenotrophomonas Maltophilia
Authors: Petrella, S. / Pernot, L. / Lascoux, D. / Forest, E. / Jarlier, V. / Sougakoff, W.
History
DepositionNov 2, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L2 BETA LACTAMASE
B: L2 BETA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,85318
Polymers58,3282
Non-polymers1,52516
Water13,205733
1
A: L2 BETA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9299
Polymers29,1641
Non-polymers7658
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: L2 BETA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9259
Polymers29,1641
Non-polymers7618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)133.216, 133.216, 93.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.885043, -0.448562, 0.124462), (-0.452213, 0.765016, -0.458535), (0.110466, -0.462107, -0.879917)
Vector: 202.3484, 77.063, 97.7365)

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Components

#1: Protein L2 BETA LACTAMASE


Mass: 29164.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STENOTROPHOMONAS MALTOPHILIA (bacteria)
Strain: 405 / Plasmid: PET29-(A+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RBQ1, beta-lactamase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 733 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE L2 MATURE PROTEIN STARTS AT RESIDUE 28 THERE ARE NO RESIDUES NUMBERED 58 AND 239

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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: 3.57 Å3/Da / Density % sol: 65.23 %
Crystal growpH: 6.5
Details: AMMONIUM SULFATE 1.5M, SODIUM CACODYLATE 0.1M PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.948
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 25, 2001
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 1.51→23.9 Å / Num. obs: 131717 / % possible obs: 99.4 % / Observed criterion σ(I): 2.5 / Redundancy: 4.8 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.7
Reflection shellResolution: 1.51→1.59 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.9 / % possible all: 96

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE STARTING MODEL USED WAS THE ONE OF L2 AT 1.85 ANGSTROM, PDB ENTRY 1N4O

1n4o


Resolution: 1.51→23.92 Å / SU B: 0.9034 / SU ML: 0.0346 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.14
RfactorNum. reflection% reflectionSelection details
Rfree0.184 5238 4 %RANDOM
Rwork0.163 ---
obs0.17 131390 99.6 %-
Displacement parametersBiso mean: 13.9 Å2
Refinement stepCycle: LAST / Resolution: 1.51→23.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 83 733 4826

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