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- PDB-1n4o: Crystal structure of the Class A beta-lactamase L2 from Stenotrop... -

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Basic information

Entry
Database: PDB / ID: 1n4o
TitleCrystal structure of the Class A beta-lactamase L2 from Stenotrophomonas maltophilia
ComponentsL2 beta-lactamase
KeywordsHYDROLASE / BETA-LACTAMASE / CLASS A / L2
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like ...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: 1.85 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: Pernot, L. / Petrella, S. / Sougakoff, W.
History
DepositionNov 1, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 The asymetric unit contains a homodimer generated by a 2-fold non-crystallographic ...BIOMOLECULE: 1 The asymetric unit contains a homodimer generated by a 2-fold non-crystallographic symmetry axis. The transformation applied to chain A gives chain B. Rotation : -0.87108099 0.47216475 0.13519730 0.47738487 0.74928564 0.45899314 0.11541899 0.46436137 -0.87809283 Translation : 37.0187 -14.5258 17.0446

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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)58,7126
Polymers58,3282
Non-polymers3844
Water5,675315
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.503, 135.503, 94.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe asymetric unit contains a homodimer generated by a 2-fold non-crystallographic symmetry axis. The transformation applied to chain A gives chain B. Rotation : -0.87108099 0.47216475 0.13519730 0.47738487 0.74928564 0.45899314 0.11541899 0.46436137 -0.87809283 Translation : 37.0187 -14.5258 17.0446

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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 / Gene: blaL2 / Plasmid: pET29(a+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9RBQ1, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 315 / 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: 3.55 Å3/Da / Density % sol: 65.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate 1.5M, sodium cacodylate 0.1M, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9485 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 25, 2001
RadiationMonochromator: Si (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9485 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 75048 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5 / Redundancy: 6.1 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.7
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.6 / Num. unique all: 10357 / % possible all: 95.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BZA

1bza


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.669 / SU ML: 0.051 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.08 / ESU R Free: 0.078 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.164 4719 -RANDOM
Rwork0.147 ---
all0.164 ---
obs0.155 70264 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4049 0 20 315 4384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0214123
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9615601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4973539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.05715701
X-RAY DIFFRACTIONr_mcbond_it1.92622688
X-RAY DIFFRACTIONr_mcangle_it3.09234288
X-RAY DIFFRACTIONr_scbond_it2.80421435
X-RAY DIFFRACTIONr_scangle_it4.39931313
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023116
X-RAY DIFFRACTIONr_chiral_restr0.1440.2652
X-RAY DIFFRACTIONr_nbd_refined0.250.31762
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.5378
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.345
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.514
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.007
RfactorNum. reflection% reflection
Rfree0.176 734 -
Rwork0.185 --
obs-11920 95.9 %

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