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- PDB-3a9x: Crystal structure of rat selenocysteine lyase -

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Basic information

Entry
Database: PDB / ID: 3a9x
TitleCrystal structure of rat selenocysteine lyase
ComponentsSelenocysteine lyase
KeywordsLYASE / selenocysteine / Pyridoxal phosphate / Transferase
Function / homology
Function and homology information


vitamin B6 binding / negative regulation of cellular response to oxidative stress / Metabolism of ingested SeMet, Sec, MeSec into H2Se / selenocysteine catabolic process / selenium compound metabolic process / selenocysteine lyase / selenocysteine lyase activity / amino acid binding / catalytic complex / response to insulin ...vitamin B6 binding / negative regulation of cellular response to oxidative stress / Metabolism of ingested SeMet, Sec, MeSec into H2Se / selenocysteine catabolic process / selenium compound metabolic process / selenocysteine lyase / selenocysteine lyase activity / amino acid binding / catalytic complex / response to insulin / lipid metabolic process / transferase activity / Golgi apparatus / protein homodimerization activity / cytosol
Similarity search - Function
434 Repressor (Amino-terminal Domain) - #50 / Cysteine desulfurase / Aminotransferase class V domain / Aminotransferase class-V / 434 Repressor (Amino-terminal Domain) / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...434 Repressor (Amino-terminal Domain) - #50 / Cysteine desulfurase / Aminotransferase class V domain / Aminotransferase class-V / 434 Repressor (Amino-terminal Domain) / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Selenocysteine lyase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOmi, R. / Hirotsu, K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Reaction mechanism and molecular basis for selenium/sulfur discrimination of selenocysteine lyase.
Authors: Omi, R. / Kurokawa, S. / Mihara, H. / Hayashi, H. / Goto, M. / Miyahara, I. / Kurihara, T. / Hirotsu, K. / Esaki, N.
History
DepositionNov 8, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Selenocysteine lyase
B: Selenocysteine lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4057
Polymers94,6262
Non-polymers7795
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-49 kcal/mol
Surface area29700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.445, 102.771, 197.753
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 Selenocysteine lyase /


Mass: 47312.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Scly / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta(DE3) / References: UniProt: Q68FT9, selenocysteine lyase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 1.5M ammonium dihydrogen phosphate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 69817 / % possible obs: 91.8 %
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.299 / Num. unique all: 6370 / % possible all: 85

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / σ(F): 0 / σ(I): 0 /
RfactorNum. reflection
Rfree0.236 -
Rwork0.197 -
obs-69695
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6021 0 45 397 6463
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.43

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