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- PDB-4rx3: A triple mutant in the omega-loop of TEM-1 beta-lactamase changes... -

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Basic information

Entry
Database: PDB / ID: 4rx3
TitleA triple mutant in the omega-loop of TEM-1 beta-lactamase changes the substrate profile via a large conformational change and an altered general base for catalysis
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / globular / beta-lactamase
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
CITRATE ANION / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsStojanoski, V. / Chow, D. / Hu, L. / Sankaran, B. / Gilbert, H. / Prasad, B.V.V. / Palzkill, T.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: A Triple Mutant in the Omega-loop of TEM-1 beta-Lactamase Changes the Substrate Profile via a Large Conformational Change and an Altered General Base for Catalysis.
Authors: Stojanoski, V. / Chow, D.C. / Hu, L. / Sankaran, B. / Gilbert, H.F. / Prasad, B.V. / Palzkill, T.
History
DepositionDec 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0722
Polymers28,8831
Non-polymers1891
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.920, 60.140, 88.770
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 TEM / IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 ...IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2


Mass: 28882.932 Da / Num. of mol.: 1 / Fragment: TEM-1 beta-lactamase / Mutation: S70G/W165Y/E166Y/P167G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.24M citrate, 25% w/v PEG 4,000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2014
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 1.39→30.54 Å / Num. all: 64012 / Num. obs: 64012 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 1.9
Reflection shell
Resolution (Å)Mean I/σ(I) obsDiffraction-ID% possible all
1.39-1.411.9199.1
7.49-30.5453.9196.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→30.54 Å / SU ML: 0.15 / σ(F): 1.92 / Phase error: 18.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1937 6207 5.09 %
Rwork0.1715 --
obs0.1726 121923 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→30.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 13 430 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072069
X-RAY DIFFRACTIONf_angle_d1.1142800
X-RAY DIFFRACTIONf_dihedral_angle_d14.227789
X-RAY DIFFRACTIONf_chiral_restr0.044319
X-RAY DIFFRACTIONf_plane_restr0.005366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.40580.31932280.29243837X-RAY DIFFRACTION98
1.4058-1.42230.29952130.28083807X-RAY DIFFRACTION99
1.4223-1.43970.30072060.27113808X-RAY DIFFRACTION98
1.4397-1.45790.26912300.25853751X-RAY DIFFRACTION98
1.4579-1.47710.27492120.24923879X-RAY DIFFRACTION99
1.4771-1.49730.23841790.23573796X-RAY DIFFRACTION99
1.4973-1.51870.26832210.23483802X-RAY DIFFRACTION99
1.5187-1.54140.2512170.22383865X-RAY DIFFRACTION99
1.5414-1.56550.21892290.21183765X-RAY DIFFRACTION99
1.5655-1.59110.19252020.20013920X-RAY DIFFRACTION99
1.5911-1.61860.19961640.18933846X-RAY DIFFRACTION100
1.6186-1.6480.18692140.18253848X-RAY DIFFRACTION99
1.648-1.67970.24032060.1923918X-RAY DIFFRACTION99
1.6797-1.7140.20782220.18493833X-RAY DIFFRACTION100
1.714-1.75120.19481990.18253881X-RAY DIFFRACTION100
1.7512-1.7920.21852150.18083867X-RAY DIFFRACTION100
1.792-1.83680.18512130.17973861X-RAY DIFFRACTION100
1.8368-1.88640.19092170.17843846X-RAY DIFFRACTION100
1.8864-1.94190.19222270.16643880X-RAY DIFFRACTION100
1.9419-2.00460.182130.16553855X-RAY DIFFRACTION100
2.0046-2.07620.20612380.16583825X-RAY DIFFRACTION100
2.0762-2.15930.17762240.15713877X-RAY DIFFRACTION100
2.1593-2.25760.21321780.15363895X-RAY DIFFRACTION100
2.2576-2.37660.1692440.16443847X-RAY DIFFRACTION100
2.3766-2.52540.17272240.16263865X-RAY DIFFRACTION100
2.5254-2.72030.19871570.16643934X-RAY DIFFRACTION100
2.7203-2.99380.19041790.16813902X-RAY DIFFRACTION100
2.9938-3.42650.18912160.16313866X-RAY DIFFRACTION100
3.4265-4.31510.15242030.14253884X-RAY DIFFRACTION100
4.3151-30.54760.171170.14973956X-RAY DIFFRACTION99

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