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- PDB-5gl9: Crystal structure of the class A beta-lactamase PenL -

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Basic information

Entry
Database: PDB / ID: 5gl9
TitleCrystal structure of the class A beta-lactamase PenL
ComponentsBeta-lactamase
KeywordsHYDROLASE / PenL / omega loop / Burkholderia
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
Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChoi, J.M. / Yi, H. / Kim, H.S. / Lee, S.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation2010-0005114 Korea, Republic Of
National Research Foundation2013R1A1A2057465 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2016
Title: High adaptability of the omega loop underlies the substrate-spectrum-extension evolution of a class A beta-lactamase, PenL
Authors: Yi, H. / Choi, J.M. / Hwang, J. / Prati, F. / Cao, T.P. / Lee, S.H. / Kim, H.S.
History
DepositionJul 10, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8623
Polymers28,6771
Non-polymers1842
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-1 kcal/mol
Surface area10910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.933, 81.637, 36.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Beta-lactamase


Mass: 28677.457 Da / Num. of mol.: 1 / Fragment: UNP residues 31-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: A8H35_31635 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A2Z4SUB5, UniProt: Q2T5A3*PLUS, beta-lactamase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.02 Å3/Da / Density % sol: 39.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 0.1M Li-sulfate, 30%(w/v) PEG 4000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2012
RadiationMonochromator: DCM Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 37054 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/av σ(I): 73.911 / Net I/σ(I): 18.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 35.682 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLJ

1ylj


Resolution: 1.5→27.8 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.23
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 1853 5.01 %Random
Rwork0.1633 ---
obs0.1647 37006 98.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 12 336 2360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062053
X-RAY DIFFRACTIONf_angle_d1.0572782
X-RAY DIFFRACTIONf_dihedral_angle_d12.024748
X-RAY DIFFRACTIONf_chiral_restr0.073319
X-RAY DIFFRACTIONf_plane_restr0.004368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5003-1.54090.18251390.16012642X-RAY DIFFRACTION97
1.5409-1.58620.18311450.15572640X-RAY DIFFRACTION99
1.5862-1.63740.19431300.15352657X-RAY DIFFRACTION98
1.6374-1.6960.20381400.15722655X-RAY DIFFRACTION98
1.696-1.76380.20671300.16542697X-RAY DIFFRACTION99
1.7638-1.84410.19581480.16732655X-RAY DIFFRACTION99
1.8441-1.94130.18831310.15862718X-RAY DIFFRACTION99
1.9413-2.06290.17991420.15962699X-RAY DIFFRACTION99
2.0629-2.22210.18431430.15552714X-RAY DIFFRACTION100
2.2221-2.44560.19791290.16382761X-RAY DIFFRACTION100
2.4456-2.79920.20791600.1732748X-RAY DIFFRACTION100
2.7992-3.52560.18421610.16652765X-RAY DIFFRACTION100
3.5256-27.80480.18251550.16532802X-RAY DIFFRACTION96

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