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- PDB-4rjy: Crystal structure of E. coli L-Threonine Aldolase in complex with... -

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Basic information

Entry
Database: PDB / ID: 4rjy
TitleCrystal structure of E. coli L-Threonine Aldolase in complex with a non-covalently uncleaved bound L-serine substrate
ComponentsLow specificity L-threonine aldolase
KeywordsLYASE / Pyridoxal-5-phosphate / threonine aldolase / aldimine / catalytic mechanism / retro-aldol cleavage / PLP-dependent enzymes
Function / homologyAspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta / SERINE / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSafo, M.K. / Chowdhury, N. / Gandhi, A.K.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Molecular basis of E. colil-threonine aldolase catalytic inactivation at low pH.
Authors: Remesh, S.G. / Ghatge, M.S. / Ahmed, M.H. / Musayev, F.N. / Gandhi, A. / Chowdhury, N. / di Salvo, M.L. / Kellogg, G.E. / Contestabile, R. / Schirch, V. / Safo, M.K.
History
DepositionOct 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Low specificity L-threonine aldolase
B: Low specificity L-threonine aldolase
C: Low specificity L-threonine aldolase
D: Low specificity L-threonine aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,58614
Polymers147,0284
Non-polymers55810
Water15,331851
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15680 Å2
ΔGint-120 kcal/mol
Surface area43890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.160, 104.880, 84.910
Angle α, β, γ (deg.)90.00, 92.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Low specificity L-threonine aldolase


Mass: 36756.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: KTE79 / Gene: A1UU_02790 / Production host: Escherichia coli (E. coli) / References: UniProt: L4EJM2
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Freshly dialyzed eTA (22 mg/mL in 20 mM potassium phosphate, pH 7.0) was incubated with L-serine (6.25 mM), precipitant solution contains 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 20% ...Details: Freshly dialyzed eTA (22 mg/mL in 20 mM potassium phosphate, pH 7.0) was incubated with L-serine (6.25 mM), precipitant solution contains 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 20% v/v 2-propoanol, 20% v/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5417 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 22, 2011
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.1→32.8 Å / Num. obs: 77165 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.91 % / Rmerge(I) obs: 0.093 / Χ2: 0.87 / Net I/σ(I): 8.4 / Scaling rejects: 24943
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.1-2.182.770.2683.82293874580.995.4
2.18-2.262.860.2544.12441276910.998.1
2.26-2.372.90.2464.22460477020.9198.2
2.37-2.492.870.2284.52482077740.998.5
2.49-2.652.90.1975.12486877210.8998.6
2.65-2.852.90.1695.72519677260.998.4
2.85-3.142.920.136.92547277870.8898.8
3.14-3.592.930.08410.22547577290.8698.3
3.59-4.522.980.05116.42558877440.8197.5
4.52-32.83.040.03921.12605178330.7597.9

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata reduction
CNSrefinement
PDB_EXTRACT3.15data extraction
CrystalCleardata collection
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2787 3871 4.9 %random
Rwork0.2125 ---
obs0.2787 76865 97.6 %-
all-77165 --
Solvent computationBsol: 78.7595 Å2
Displacement parametersBiso max: 113.59 Å2 / Biso mean: 27.2876 Å2 / Biso min: 1.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.873 Å20 Å20.122 Å2
2---3.987 Å20 Å2
3---1.114 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10252 0 34 851 11137
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.507
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3llp.par
X-RAY DIFFRACTION4llp-patch.par
X-RAY DIFFRACTION5sen.par

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