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- PDB-4zdo: The crystal structure of T325S mutant of human SepSecS in complex... -

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Basic information

Entry
Database: PDB / ID: 4zdo
TitleThe crystal structure of T325S mutant of human SepSecS in complex with selenocysteine tRNA (tRNASec)
Components
  • O-phosphoseryl-tRNA(Sec) selenium transferase
  • selenocysteine tRNA
KeywordsTransferase/RNA / selenocysteine / tRNA / mutation / pyridoxal phosphate / Transferase-RNA complex
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 / Selenocysteine synthesis / tRNA binding / nucleus / cytosol / 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 / Peroxidases heam-ligand binding site / 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 ...Arc Repressor Mutant, subunit A - #2160 / O-phosphoseryl-tRNA(Sec) selenium transferase / SepSecS/SepCysS family / O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS / Peroxidases heam-ligand binding site / 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
Chem-PLR / PHOSPHATE ION / : / RNA / RNA (> 10) / O-phosphoseryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsFrench, R.L. / Simonovic, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097042 United States
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis for early-onset neurological disorders caused by mutations in human selenocysteine synthase.
Authors: Puppala, A.K. / French, R.L. / Matthies, D. / Baxa, U. / Subramaniam, S. / Simonovic, M.
History
DepositionApr 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: O-phosphoseryl-tRNA(Sec) selenium transferase
C: O-phosphoseryl-tRNA(Sec) selenium transferase
D: O-phosphoseryl-tRNA(Sec) selenium transferase
E: selenocysteine tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,43013
Polymers251,1175
Non-polymers1,3138
Water8,449469
1
A: O-phosphoseryl-tRNA(Sec) selenium transferase
B: O-phosphoseryl-tRNA(Sec) selenium transferase
E: selenocysteine tRNA
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)252,43013
Polymers251,1175
Non-polymers1,3138
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_755-x+y+2,y,-z+1/31
2
C: O-phosphoseryl-tRNA(Sec) selenium transferase
D: O-phosphoseryl-tRNA(Sec) selenium transferase
E: selenocysteine tRNA
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)252,43013
Polymers251,1175
Non-polymers1,3138
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-y+1,-x+1,-z+2/31
Unit cell
Length a, b, c (Å)166.238, 166.238, 238.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-1139-

HOH

21B-1159-

HOH

31B-1190-

HOH

41C-1169-

HOH

51D-1170-

HOH

61D-1177-

HOH

Detailssymmetry operation on chains A, B and conformer A of chain E: X, X-Y, -Z (0 -1 0); or on chains C and D and conformer B of chain E: -X+Y, Y, -Z+1/3 (0 0 0)

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Components

#1: Protein
O-phosphoseryl-tRNA(Sec) selenium transferase / Liver-pancreas antigen / LP / SLA-p35 / SLA/LP autoantigen / Selenocysteine synthase / Sec synthase ...Liver-pancreas antigen / LP / SLA-p35 / SLA/LP autoantigen / Selenocysteine synthase / Sec synthase / Selenocysteinyl-tRNA(Sec) synthase / Sep-tRNA:Sec-tRNA synthase / SepSecS / Soluble liver antigen / SLA / UGA suppressor tRNA-associated protein / tRNA(Ser/Sec)-associated antigenic protein


Mass: 55787.188 Da / Num. of mol.: 4 / Mutation: T325S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPSECS, TRNP48 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HD40, O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase
#2: RNA chain selenocysteine tRNA


Mass: 27968.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / References: GenBank: 28372595
#3: Chemical
ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H12NO5P
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 469 / 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: 3.78 Å3/Da / Density % sol: 67.44 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.1M Na-cacodylate, pH 6.4 0.24M lithium citrate 10-12% (w/v) PEG 3,350
PH range: 6.4

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 133611 / % possible obs: 90.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 52.34 Å2 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.059 / Rrim(I) all: 0.161 / Χ2: 1.405 / Net I/av σ(I): 11.394 / Net I/σ(I): 5 / Num. measured all: 1085896
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Χ2% possible allRpim(I) allRmerge(I) obsRrim(I) all
2.4-2.441.525680.030.70635
2.44-2.491.836330.0730.95949.8
2.49-2.532.348840.1160.93667.1
2.53-2.593.257790.1880.81879.4
2.59-2.644.265800.2950.87389.60.939
2.64-2.75.370940.4530.81997.50.698
2.7-2.776.773490.5811.00899.50.527
2.77-2.857.772590.7230.8271000.419
2.85-2.938.573030.8440.8471000.3030.8390.893
2.93-3.029.173470.90.8481000.2350.6740.714
3.02-3.139.273570.9380.9021000.1750.5060.536
3.13-3.269.373180.9570.9621000.140.4080.432
3.26-3.419.473080.9691.0421000.110.3220.341
3.41-3.589.673430.9841.1521000.0780.2290.242
3.58-3.819.873360.9891.3141000.0610.1830.193
3.81-4.110.173790.9921.581000.0460.140.148
4.1-4.5210.573600.9941.8971000.0370.1140.12
4.52-5.171174000.9952.1881000.0340.1070.112
5.17-6.5111.374210.9942.3631000.0370.1190.124
6.51-501175930.9952.38699.90.0190.060.063

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HL2

3hl2


Resolution: 2.65→49.492 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 4082 3.75 %
Rwork0.1982 --
obs0.1996 108892 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→49.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13541 1590 80 469 15680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01517399
X-RAY DIFFRACTIONf_angle_d1.04424276
X-RAY DIFFRACTIONf_dihedral_angle_d13.3386780
X-RAY DIFFRACTIONf_chiral_restr0.0562925
X-RAY DIFFRACTIONf_plane_restr0.0062561

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