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- PDB-5glb: Crystal structure of the class A beta-lactamase PenL-tTR10 in com... -

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Basic information

Entry
Database: PDB / ID: 5glb
TitleCrystal structure of the class A beta-lactamase PenL-tTR10 in complex with CBA
ComponentsBeta-lactamase
KeywordsHYDROLASE / PenL-tTR10 / omega loop
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-CB4 / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Advisory / Database references ...Advisory / Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_validate_close_contact ...entity_src_gen / pdbx_validate_close_contact / struct_conn / 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)30,0952
Polymers29,7651
Non-polymers3301
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-4 kcal/mol
Surface area11130 Å2
Unit cell
Length a, b, c (Å)70.059, 92.881, 34.993
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: 29764.574 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-CB4 / PINACOL[[2-AMINO-ALPHA-(1-CARBOXY-1-METHYLETHOXYIMINO)-4-THIAZOLEACETYL]AMINO]METHANEBORONATE


Mass: 330.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15BN4O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 1.94 Å3/Da / Density % sol: 36.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 30% PEGMME 2000, 0.1M K-thiocyanate, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 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: 1.6→50 Å / Num. obs: 30982 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.072 / Net I/av σ(I): 44.692 / Net I/σ(I): 12.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 9.714 / % possible all: 100

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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: 5GL9

5gl9


Resolution: 1.6→32.776 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.08
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 1561 5.05 %random
Rwork0.1615 ---
obs0.1634 30932 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→32.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 22 255 2289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072064
X-RAY DIFFRACTIONf_angle_d1.2132799
X-RAY DIFFRACTIONf_dihedral_angle_d15.506766
X-RAY DIFFRACTIONf_chiral_restr0.071319
X-RAY DIFFRACTIONf_plane_restr0.004369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5998-1.65140.22351340.16132595X-RAY DIFFRACTION100
1.6514-1.71040.21741270.16432648X-RAY DIFFRACTION100
1.7104-1.77890.24651630.16972601X-RAY DIFFRACTION100
1.7789-1.85990.21191270.16252643X-RAY DIFFRACTION100
1.8599-1.95790.20791500.14982651X-RAY DIFFRACTION100
1.9579-2.08050.18751520.15272615X-RAY DIFFRACTION100
2.0805-2.24120.19181040.14932707X-RAY DIFFRACTION100
2.2412-2.46660.1841540.15732651X-RAY DIFFRACTION100
2.4666-2.82340.20111590.1692669X-RAY DIFFRACTION100
2.8234-3.55650.21321390.17032742X-RAY DIFFRACTION100
3.5565-32.78280.18281520.16212849X-RAY DIFFRACTION100

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