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- PDB-6nvt: Crystal structure of TLA-1 extended spectrum Beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 6nvt
TitleCrystal structure of TLA-1 extended spectrum Beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / Lactamase / Antibiotic / Resistance
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 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,14079
Polymers123,7904
Non-polymers5,35075
Water18,6641036
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,36421
Polymers30,9471
Non-polymers1,41620
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,01015
Polymers30,9471
Non-polymers1,06214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,46322
Polymers30,9471
Non-polymers1,51621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,30321
Polymers30,9471
Non-polymers1,35620
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.060, 99.010, 99.700
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase


Mass: 30947.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(DE3) / Gene: tla-1 / Plasmid: pJ411 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X6W1, beta-lactamase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1036 / 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: 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 mMSodium 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: 0.979131 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 30, 2017 / Details: Sagitally focusing second 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: 0.979131 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 97662 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.01 % / Biso Wilson estimate: 39.639 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.077 / Rsym value: 0.069 / Net I/σ(I): 4.08
Reflection shellResolution: 2.2→2.3 Å / Mean I/σ(I) obs: 4.08 / Num. unique obs: 12124 / CC1/2: 0.839 / Rrim(I) all: 0.647 / Rsym value: 0.579 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+25 / Resolution: 2.2→35.148 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 4857 4.98 %Random 5 percent
Rwork0.1813 92757 --
obs0.1826 97614 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.12 Å2 / Biso mean: 39.7915 Å2 / Biso min: 18.22 Å2
Refinement stepCycle: final / Resolution: 2.2→35.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8712 0 306 1039 10057
Biso mean--63.29 46.48 -
Num. residues----1104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0279237
X-RAY DIFFRACTIONf_angle_d1.81112485
X-RAY DIFFRACTIONf_chiral_restr0.21405
X-RAY DIFFRACTIONf_plane_restr0.0131567
X-RAY DIFFRACTIONf_dihedral_angle_d4.8177617
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2250.30541770.276430673244100
2.225-2.25120.28711620.271730783240100
2.2512-2.27860.31881680.260129973165100
2.2786-2.30750.27411540.251631703324100
2.3075-2.33780.26381600.246330453205100
2.3378-2.36980.26371460.238530833229100
2.3698-2.40370.24321510.235531193270100
2.4037-2.43960.29511680.232130493217100
2.4396-2.47770.29331910.235430743265100
2.4777-2.51830.24661890.226630243213100
2.5183-2.56170.29831520.220431303282100
2.5617-2.60830.31720.215531283300100
2.6083-2.65840.281570.215530013158100
2.6584-2.71260.22311610.220530833244100
2.7126-2.77160.25321680.218230943262100
2.7716-2.83610.22271590.22230943253100
2.8361-2.90690.24491610.217730673228100
2.9069-2.98550.25521460.210731353281100
2.9855-3.07330.24151550.211330973252100
3.0733-3.17240.21821580.198930733231100
3.1724-3.28570.19321310.186831343265100
3.2857-3.41720.18781350.17531583293100
3.4172-3.57260.20751820.159530683250100
3.5726-3.76070.16351580.143230613219100
3.7607-3.9960.17161780.135530973275100
3.996-4.30410.12411540.123931333287100
4.3041-4.73630.17741030.118931563259100
4.7363-5.41950.17031910.145731143305100
5.4195-6.81980.20071510.189431173268100
6.8198-35.1520.16352190.1663111333098

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