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- PDB-6afo: Crystal structure of class A b-lactamase, PenL, variant Asn136Asp... -

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Basic information

Entry
Database: PDB / ID: 6afo
TitleCrystal structure of class A b-lactamase, PenL, variant Asn136Asp, from Burkholderia thailandensis
ComponentsBeta-lactamase
KeywordsHYDROLASE / extended-spectrum beta-lactam / Asn136Asp / PenL / Burkhodelria
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: 1.399 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)57,3572
Polymers57,3572
Non-polymers00
Water13,025723
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)28,6781
Polymers28,6781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)28,6781
Polymers28,6781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.986, 92.723, 68.878
Angle α, β, γ (deg.)90.00, 92.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 28678.441 Da / Num. of mol.: 2 / Mutation: N136D
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 723 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN136D is isolated from bacterial colonies that resisted to antibiotic, thus the mutation was not ...N136D 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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium acetate pH 5.0 200 mM sodium chloride 25% (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 5, 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: 1.399→50 Å / Num. obs: 86131 / % possible obs: 99 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 40.23
Reflection shellResolution: 1.399→1.42 Å / Rmerge(I) obs: 0.271 / Num. unique obs: 4254

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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: 1.399→31.772 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 16.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1739 4313 5.01 %
Rwork0.1473 --
obs0.1487 86034 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.399→31.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 0 723 4747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144248
X-RAY DIFFRACTIONf_angle_d1.595777
X-RAY DIFFRACTIONf_dihedral_angle_d11.5491568
X-RAY DIFFRACTIONf_chiral_restr0.069658
X-RAY DIFFRACTIONf_plane_restr0.008774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3991-1.4150.21961390.17782613X-RAY DIFFRACTION97
1.415-1.43170.21881300.18122723X-RAY DIFFRACTION100
1.4317-1.44910.21971340.18212739X-RAY DIFFRACTION100
1.4491-1.46750.23241390.18292725X-RAY DIFFRACTION100
1.4675-1.48680.21411500.16622700X-RAY DIFFRACTION100
1.4868-1.50720.18851390.16782744X-RAY DIFFRACTION100
1.5072-1.52870.20751460.16042747X-RAY DIFFRACTION100
1.5287-1.55150.17761510.15342686X-RAY DIFFRACTION100
1.5515-1.57580.18691390.15312738X-RAY DIFFRACTION100
1.5758-1.60160.19871420.15122735X-RAY DIFFRACTION100
1.6016-1.62920.16741570.15162682X-RAY DIFFRACTION100
1.6292-1.65880.18361500.15192733X-RAY DIFFRACTION100
1.6588-1.69070.20491520.15252704X-RAY DIFFRACTION100
1.6907-1.72520.19011290.15542730X-RAY DIFFRACTION100
1.7252-1.76280.19721350.15352760X-RAY DIFFRACTION100
1.7628-1.80380.20661400.15812714X-RAY DIFFRACTION100
1.8038-1.84890.16691300.15062777X-RAY DIFFRACTION100
1.8489-1.89880.16531520.14952676X-RAY DIFFRACTION100
1.8988-1.95470.19141470.14522756X-RAY DIFFRACTION100
1.9547-2.01780.15331540.14092686X-RAY DIFFRACTION100
2.0178-2.08990.15141300.14572752X-RAY DIFFRACTION100
2.0899-2.17360.15221400.13652745X-RAY DIFFRACTION100
2.1736-2.27250.17351630.14252694X-RAY DIFFRACTION100
2.2725-2.39220.16831470.14972739X-RAY DIFFRACTION100
2.3922-2.5420.17631410.1512744X-RAY DIFFRACTION100
2.542-2.73820.18611480.14752729X-RAY DIFFRACTION100
2.7382-3.01360.17541590.15072720X-RAY DIFFRACTION100
3.0136-3.44920.16231520.13592747X-RAY DIFFRACTION100
3.4492-4.34390.14941410.12352765X-RAY DIFFRACTION100
4.3439-31.78030.14761370.14412718X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 14.2999 Å / Origin y: 8.0324 Å / Origin z: 17.2013 Å
111213212223313233
T0.0824 Å2-0.0014 Å20.0026 Å2-0.0616 Å2-0.0034 Å2--0.0722 Å2
L0.0675 °20.0096 °2-0.0173 °2-0.0024 °2-0.0228 °2--0.1301 °2
S-0.0015 Å °0.0055 Å °0.0027 Å °-0.0012 Å °-0.0029 Å °0.0046 Å °0.0054 Å °-0.0023 Å °0.0038 Å °
Refinement TLS groupSelection details: all

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