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- PDB-2e7i: Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobu... -

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Basic information

Entry
Database: PDB / ID: 2e7i
TitleCrystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus
ComponentsSep-tRNA:Cys-tRNA synthase
KeywordsLYASE / seven-stranded bete-strand / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


O-phospho-L-seryl-tRNA:Cys-tRNA synthase / Sep-tRNA:Cys-tRNA synthase activity / translation
Similarity search - Function
O-phosphoseryl-tRNA:Cys-tRNA synthase, archaea / SepSecS/SepCysS family / O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS / 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 ...O-phosphoseryl-tRNA:Cys-tRNA synthase, archaea / SepSecS/SepCysS family / O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / O-phospho-L-seryl-tRNA:Cys-tRNA synthase 1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsFukunaga, R. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Insights into the Second Step of RNA-dependent Cysteine Biosynthesis in Archaea: Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus
Authors: Fukunaga, R. / Yokoyama, S.
History
DepositionJan 10, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sep-tRNA:Cys-tRNA synthase
B: Sep-tRNA:Cys-tRNA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7148
Polymers83,9862
Non-polymers7276
Water1,29772
1
A: Sep-tRNA:Cys-tRNA synthase
hetero molecules

A: Sep-tRNA:Cys-tRNA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,05710
Polymers83,9862
Non-polymers1,0718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area5470 Å2
ΔGint-93 kcal/mol
Surface area27890 Å2
MethodPISA, PQS
2
B: Sep-tRNA:Cys-tRNA synthase
hetero molecules

B: Sep-tRNA:Cys-tRNA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3716
Polymers83,9862
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_435x-y-1,-y-2,-z1
Buried area4480 Å2
ΔGint-101 kcal/mol
Surface area28090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)220.663, 220.663, 92.929
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Sep-tRNA:Cys-tRNA synthase / Hypothetical protein AF_0028


Mass: 41993.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pet26b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O30207
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.89 Å3/Da / Density % sol: 68.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 80mM sodium acetate buffer (pH 4.4), 160mM NaCl, 1.00M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.995 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.995 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 27158 / Num. obs: 27104 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Rmerge(I) obs: 0.16 / Rsym value: 0.16 / Net I/σ(I): 12.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2645 / Rsym value: 0.508 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3→47.44 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 6060723.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1318 4.9 %RANDOM
Rwork0.271 ---
obs0.271 27104 99.7 %-
all-27158 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.8315 Å2 / ksol: 0.322945 e/Å3
Displacement parametersBiso mean: 61.5 Å2
Baniso -1Baniso -2Baniso -3
1-12.03 Å219.05 Å20 Å2
2--12.03 Å20 Å2
3----24.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.83 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 3→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5474 0 40 72 5586
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it5.841.5
X-RAY DIFFRACTIONc_mcangle_it92
X-RAY DIFFRACTIONc_scbond_it8.542
X-RAY DIFFRACTIONc_scangle_it12.352.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.389 212 4.8 %
Rwork0.362 4181 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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