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- PDB-6afn: Crystal structure of class A b-lactamase, PenL, variant Cys69Tyr,... -

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Basic information

Entry
Database: PDB / ID: 6afn
TitleCrystal structure of class A b-lactamase, PenL, variant Cys69Tyr, from Burkholderia thailandensis, in complex with ceftazidime-like boronic acid
ComponentsBeta-lactamase
KeywordsHYDROLASE / extended-spectrum beta-lactam / Cys69Tyr / PenL / Burkhodelria / ceftazidime-like boronic acid HYDROLASE
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: 1.4 Å
AuthorsCao, T.-P. / Choi, J.M. / Lee, S.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2016R1D1A1B03932717 Korea, Republic Of
CitationJournal: Front Mol Biosci / Year: 2020
Title: Non-catalytic-Region Mutations Conferring Transition of Class A beta-Lactamases Into ESBLs.
Authors: Cao, T.-P. / Yi, H. / Dhanasingh, I. / Ghosh, S. / Choi, J.M. / Lee, K.H. / Ryu, S. / Kim, H.S. / Lee, S.H.
History
DepositionAug 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_mutation / _entity_src_gen.gene_src_strain ..._entity.pdbx_mutation / _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_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.2Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 22, 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)29,1603
Polymers28,7371
Non-polymers4222
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint0 kcal/mol
Surface area11100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.660, 53.238, 122.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase


Mass: 28737.488 Da / Num. of mol.: 1 / Mutation: C69Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: A8H35_31635 / Production host: Escherichia coli BL21(DE3) (bacteria)
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC69Y is isolated from bacterial colonies that resisted to antibiotic, thus the mutation was not ...C69Y is isolated from bacterial colonies that resisted to antibiotic, thus the mutation was not actually engineered using artificial method like site-directed mutagenesis.

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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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 200 mM sodium acetate trihydrate 20% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97954 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: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 50752 / % possible obs: 99.6 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 43.78
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.256 / Num. unique obs: 2479

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GL9

5gl9


Resolution: 1.4→31.282 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 13.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1695 2560 5.06 %
Rwork0.147 --
obs0.1481 50592 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→31.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 28 369 2415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062174
X-RAY DIFFRACTIONf_angle_d1.1042967
X-RAY DIFFRACTIONf_dihedral_angle_d12.846800
X-RAY DIFFRACTIONf_chiral_restr0.041337
X-RAY DIFFRACTIONf_plane_restr0.005397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4003-1.42720.1551370.14442614X-RAY DIFFRACTION99
1.4272-1.45640.16871350.14162591X-RAY DIFFRACTION99
1.4564-1.4880.1521470.13932677X-RAY DIFFRACTION99
1.488-1.52270.15791370.14052582X-RAY DIFFRACTION99
1.5227-1.56070.15861520.13982637X-RAY DIFFRACTION100
1.5607-1.60290.15311380.1392639X-RAY DIFFRACTION99
1.6029-1.65010.18531500.13312622X-RAY DIFFRACTION99
1.6501-1.70330.14821400.13892645X-RAY DIFFRACTION100
1.7033-1.76420.15891390.14312674X-RAY DIFFRACTION100
1.7642-1.83490.17631590.14472649X-RAY DIFFRACTION100
1.8349-1.91830.16761340.1422667X-RAY DIFFRACTION100
1.9183-2.01950.18441450.14282662X-RAY DIFFRACTION100
2.0195-2.1460.17181410.1432693X-RAY DIFFRACTION100
2.146-2.31160.16811420.14172679X-RAY DIFFRACTION100
2.3116-2.54410.17671200.15312728X-RAY DIFFRACTION100
2.5441-2.91210.15531330.16012721X-RAY DIFFRACTION100
2.9121-3.6680.17241590.14772742X-RAY DIFFRACTION100
3.668-31.28990.181520.15422810X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 6.0492 Å / Origin y: -7.3752 Å / Origin z: -15.5077 Å
111213212223313233
T0.0492 Å2-0.0049 Å2-0.0006 Å2-0.0557 Å20.0094 Å2--0.0528 Å2
L0.5693 °2-0.1523 °20.0268 °2-0.7254 °20.1419 °2--0.682 °2
S0.0019 Å °0.03 Å °0.0454 Å °-0.0273 Å °0.0112 Å °-0.0249 Å °-0.0239 Å °0.0166 Å °0.0233 Å °
Refinement TLS groupSelection details: all

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