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- PDB-3bca: Crystal structure of mouse selenocysteine synthase, sodium iodide soak -

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Basic information

Entry
Database: PDB / ID: 3bca
TitleCrystal structure of mouse selenocysteine synthase, sodium iodide soak
ComponentsO-phosphoseryl-tRNA(Sec) selenium transferase
KeywordsTRANSFERASE / disorder-order transition / phosphate-loop / pyridoxal phosphate / selenocysteine synthase (SecS / SepSecS) / soluble liver antigen/liver and pancreas antigen (SLA/LP) / Protein biosynthesis / Selenium
Function / homology
Function and homology information


O-phosphoseryl-tRNA(Sec) selenium transferase activity / O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase / conversion of seryl-tRNAsec to selenocys-tRNAsec / selenocysteine incorporation / tRNA binding / nucleus / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #2160 / O-phosphoseryl-tRNA(Sec) selenium transferase / 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, major domain / Pyridoxal phosphate-dependent transferase ...Arc Repressor Mutant, subunit A - #2160 / O-phosphoseryl-tRNA(Sec) selenium transferase / 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, major domain / Pyridoxal phosphate-dependent transferase / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / O-phosphoseryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.25 Å
AuthorsGanichkin, O.M. / Wahl, M.C.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure and catalytic mechanism of eukaryotic selenocysteine synthase.
Authors: Ganichkin, O.M. / Xu, X.M. / Carlson, B.A. / Mix, H. / Hatfield, D.L. / Gladyshev, V.N. / Wahl, M.C.
History
DepositionNov 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-phosphoseryl-tRNA(Sec) selenium transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,84863
Polymers49,9801
Non-polymers7,86862
Water4,756264
1
A: O-phosphoseryl-tRNA(Sec) selenium transferase
hetero molecules

A: O-phosphoseryl-tRNA(Sec) selenium transferase
hetero molecules

A: O-phosphoseryl-tRNA(Sec) selenium transferase
hetero molecules

A: O-phosphoseryl-tRNA(Sec) selenium transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,391252
Polymers199,9194
Non-polymers31,472248
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.222, 138.371, 141.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-598-

HOH

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Components

#1: Protein O-phosphoseryl-tRNA(Sec) selenium transferase / Selenocysteine synthase / Sec synthase / Selenocysteinyl-tRNA(Sec) synthase / Sep-tRNA:Sec-tRNA ...Selenocysteine synthase / Sec synthase / Selenocysteinyl-tRNA(Sec) synthase / Sep-tRNA:Sec-tRNA synthase / SepSecS / UGA suppressor tRNA-associated protein


Mass: 49979.812 Da / Num. of mol.: 1 / Fragment: Elastase-resistant fragment: Residues 19-468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sepsecs, D5Ertd135e / Plasmid: pETM-13-secS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta2 / References: UniProt: Q6P6M7, EC: 2.9.1.-
#2: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 62 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 11 % (v/v) Ethylene glycol, soaked in 0.5 M NaI, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 27, 2007 / Details: Osmic Mirrors
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 52394 / Num. obs: 52394 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 32.2 Å2 / Rsym value: 0.093 / Net I/σ(I): 13.4
Reflection shellResolution: 2.25→2.38 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.354 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SIRAS / Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.454 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used in phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23566 1382 5 %RANDOM
Rwork0.1826 ---
obs0.18526 26104 98.01 %-
all-26104 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.036 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.25 Å2
Refine analyzeLuzzati coordinate error obs: 0.247 Å
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 62 264 3721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223506
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.974742
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6315443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99323.378148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68915627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.951526
X-RAY DIFFRACTIONr_chiral_restr0.0770.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022607
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.21719
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22439
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.2111
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4231.52207
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.78223534
X-RAY DIFFRACTIONr_scbond_it1.41131378
X-RAY DIFFRACTIONr_scangle_it2.3584.51208
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 96 -
Rwork0.2 1839 -
obs--96.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.41190.39420.44581.28350.81022.08090.0511-0.05590.0504-0.0142-0.0301-0.212-0.03190.2292-0.02110.0072-0.01890.0133-0.11660.0079-0.119843.3361.275-0.14
20.47310.0393-0.18840.9111-0.33770.77160.0285-0.0561-0.06190.0692-0.0108-0.07380.08930.0481-0.01770.0284-0.0052-0.0364-0.12360.0116-0.172432.8437.10515.523
31.8336-0.2982-0.7851.3218-0.11741.50930.05180.1395-0.09920.01170.02960.1853-0.0882-0.297-0.08140.0201-0.01050.0166-0.07270.0497-0.19139.0445.17125.901
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA23 - 1065 - 88
2X-RAY DIFFRACTION2AA107 - 34589 - 327
3X-RAY DIFFRACTION3AA346 - 466328 - 448

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