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- PDB-3bcb: Crystal structure of mouse selenocysteine synthase, sodium phosph... -

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Basic information

Entry
Database: PDB / ID: 3bcb
TitleCrystal structure of mouse selenocysteine synthase, sodium phosphate 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
PHOSPHATE ION / O-phosphoseryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,2054
Polymers49,9801
Non-polymers2253
Water9,152508
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)200,82116
Polymers199,9194
Non-polymers90212
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 area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.231, 138.974, 141.821
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-516-

HOH

21A-674-

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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 57.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 11 % Ethylene glycol, soaked in 0.5 M Na phosphate, 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: Oct 4, 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: 1.85→50 Å / Num. all: 49649 / Num. obs: 49649 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 23.9 Å2 / Rsym value: 0.046 / Net I/σ(I): 16.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.542 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BC8
Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.958 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20265 2517 5.1 %RANDOM
Rwork0.16606 ---
obs0.16784 47049 98.75 %-
all-47049 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.136 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2--0.28 Å20 Å2
3----1.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.115 Å
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3461 0 11 508 3980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223669
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9714981
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.385474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68723.377154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32315657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9471528
X-RAY DIFFRACTIONr_chiral_restr0.0760.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022757
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21853
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.22556
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2431
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.2122
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5591.52380
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88923723
X-RAY DIFFRACTIONr_scbond_it1.60431435
X-RAY DIFFRACTIONr_scangle_it2.5554.51258
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 180 -
Rwork0.341 3157 -
obs--93.03 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.79960.06910.04731.02480.57861.59530.0291-0.04370.018-0.02010.029-0.1678-0.01350.1804-0.0581-0.0613-0.01910.0115-0.0196-0.0050.010543.36359.471-0.404
20.42520.0613-0.14290.6429-0.23470.60360.0223-0.0499-0.04040.0371-0.0032-0.03970.06160.0577-0.0191-0.02820.0018-0.0277-0.01840.0084-0.024132.94137.3615.512
31.3929-0.2613-0.74041.28710.38841.50430.06260.09640.00820.06530.00390.1758-0.0675-0.2298-0.0664-0.041-0.00260.0191-0.00630.0572-0.04329.20945.33926.035
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 - 467328 - 449

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