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- PDB-6nvu: Crystal structure of TLA-1 extended spectrum Beta-lactamase in co... -

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Basic information

Entry
Database: PDB / ID: 6nvu
TitleCrystal structure of TLA-1 extended spectrum Beta-lactamase in complex with Clavulanic Acid
ComponentsBeta-lactamase
Keywordshydrolase/antibiotic / Lactamase / Antibiotic / Resistance / HYDROLASE / hydrolase-antibiotic complex
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
ACETATE ION / Chem-J01 / Chem-L4A / Chem-TEM / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRudino-Pinera, E. / Cifuentes-Castro, V.H. / Rodriguez-Almazan, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: The crystal structure of ESBL TLA-1 in complex with clavulanic acid reveals a second acylation site.
Authors: Cifuentes-Castro, V. / Rodriguez-Almazan, C. / Silva-Sanchez, J. / Rudino-Pinera, E.
History
DepositionFeb 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 11, 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_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)32,18612
Polymers31,0621
Non-polymers1,12411
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.640, 98.640, 100.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase / ESBL TLA-1


Mass: 31062.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tla-1 / Plasmid: pJ411 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X6W1, beta-lactamase

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Non-polymers , 8 types, 173 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-TEM / N-(2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-TRANSPROPENYL)AMINE


Mass: 157.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-L4A / 2,5-bis(2-hydroxyethyl)-1,3-oxazole-4-carboxylic acid / Clavulanic Acid, opened form


Mass: 201.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-J01 / (2R,3Z,5R)-3-(2-HYDROXYETHYLIDENE)-7-OXO-4-OXA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID / CLAVULANIC ACID


Mass: 199.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.93 Å3/Da / Density % sol: 68.71 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2.4 M Ammonium sulfate, 100 mM Sodium Phosphate dibasic/Citric Acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791932 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 18, 2017 / Details: Sagitally focusing 2nd crystal
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator: water cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791932 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 17306 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 37.502 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.018 / Rrim(I) all: 0.0191 / Net I/σ(I): 16.23
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1930 / CC1/2: 0.858 / Rrim(I) all: 1.152 / Rsym value: 1.12 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+25 / Resolution: 2.5→35.182 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.69
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 918 5.32 %Random 5 percent
Rwork0.2012 ---
obs0.2045 17257 97.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.43 Å2 / Biso mean: 37.1056 Å2 / Biso min: 19.41 Å2
Refinement stepCycle: final / Resolution: 2.5→35.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 73 162 2420
Biso mean--51.34 38.74 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072295
X-RAY DIFFRACTIONf_angle_d0.9163093
X-RAY DIFFRACTIONf_chiral_restr0.053352
X-RAY DIFFRACTIONf_plane_restr0.005388
X-RAY DIFFRACTIONf_dihedral_angle_d7.6371387
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.63180.33251890.282422772466100
2.6318-2.79660.30911210.263423662487100
2.7966-3.01240.29731450.248323392484100
3.0124-3.31540.3292950.221824012496100
3.3154-3.79460.3025950.21232044213985
3.7946-4.77890.20351460.15372339248597
4.7789-35.1850.22581270.16725732700100

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