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- PDB-4zdl: The crystal structure of the T325S mutant of the human holo SepSecS -

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Basic information

Entry
Database: PDB / ID: 4zdl
TitleThe crystal structure of the T325S mutant of the human holo SepSecS
ComponentsO-phosphoseryl-tRNA(Sec) selenium transferase
KeywordsTRANSFERASE / selenocysteine / pyridoxal phosphate / mutation
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
CITRATE ANION / Chem-PLR / O-phosphoseryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,2305
Polymers111,5742
Non-polymers6553
Water9,548530
1
A: O-phosphoseryl-tRNA(Sec) selenium transferase
B: O-phosphoseryl-tRNA(Sec) selenium transferase
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)224,46010
Polymers223,1494
Non-polymers1,3116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area23160 Å2
ΔGint-110 kcal/mol
Surface area56210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.016, 83.151, 193.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Components on special symmetry positions
IDModelComponents
11A-1186-

HOH

21A-1232-

HOH

31A-1385-

HOH

41B-1172-

HOH

51B-1212-

HOH

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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.: 2 / Mutation: T325S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPSECS, TRNP48 / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21
References: UniProt: Q9HD40, O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase
#2: Chemical ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12NO5P
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / Details: 0.28-0.34 M lithium citrate 16-18% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 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: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 44262 / % possible obs: 85 % / Redundancy: 14.2 % / Biso Wilson estimate: 39.08 Å2 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.047 / Rrim(I) all: 0.19 / Χ2: 1.17 / Net I/av σ(I): 12.621 / Net I/σ(I): 5.2 / Num. measured all: 628475
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.25-2.294.70.98310410.6310.4330.45140.9
2.29-2.335.112000.5520.4230.47346.6
2.33-2.385.80.86113630.660.3420.47453.10.933
2.38-2.426.60.8115470.6770.3050.50860.30.871
2.42-2.487.60.82117530.6750.2920.51268.70.876
2.48-2.538.70.74719550.8280.2480.54576.80.79
2.53-2.610.20.7120890.8330.220.5780.10.746
2.6-2.6711.30.66322330.8590.1940.61687.10.693
2.67-2.7513.30.63423580.8780.1740.654920.66
2.75-2.8315.50.59624190.9440.1520.65793.70.617
2.83-2.94160.48125280.9560.1210.75297.40.497
2.94-3.0516.40.40925960.9690.1030.84599.70.423
3.05-3.1916.90.33825740.9790.0850.96299.90.349
3.19-3.3617.10.28825860.9840.0721.0911000.297
3.36-3.5717.20.21526200.9910.0531.4671000.221
3.57-3.8517.40.1726040.9950.0421.5791000.175
3.85-4.2317.50.14326320.9960.0351.6361000.148
4.23-4.8517.70.12626580.9960.0311.8331000.13
4.85-6.118.40.12526790.9970.031.7161000.129
6.1-5017.80.08428270.9980.0211.72899.90.087

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Processing

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

3hl2


Resolution: 2.26→46.224 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 2192 4.97 %random selection
Rwork0.1629 41922 --
obs0.1658 44114 84.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.72 Å2 / Biso mean: 43.9471 Å2 / Biso min: 14.89 Å2
Refinement stepCycle: final / Resolution: 2.26→46.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6728 0 48 532 7308
Biso mean--52.37 47.7 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087087
X-RAY DIFFRACTIONf_angle_d1.1079643
X-RAY DIFFRACTIONf_chiral_restr0.041114
X-RAY DIFFRACTIONf_plane_restr0.0041240
X-RAY DIFFRACTIONf_dihedral_angle_d13.6332628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2604-2.30950.30971070.26431152X-RAY DIFFRACTION39
2.3095-2.36330.3061070.25481545X-RAY DIFFRACTION48
2.3633-2.42240.30231070.24741694X-RAY DIFFRACTION56
2.4224-2.48790.34351090.2392035X-RAY DIFFRACTION67
2.4879-2.56110.32481100.22262369X-RAY DIFFRACTION77
2.5611-2.64370.22921100.22652529X-RAY DIFFRACTION82
2.6437-2.73820.30562200.22212669X-RAY DIFFRACTION89
2.7382-2.84780.29341090.22062918X-RAY DIFFRACTION93
2.8478-2.97740.27052060.2082948X-RAY DIFFRACTION97
2.9774-3.13430.26121240.17933095X-RAY DIFFRACTION100
3.1343-3.33070.23421100.16873160X-RAY DIFFRACTION100
3.3307-3.58770.23952200.15133045X-RAY DIFFRACTION100
3.5877-3.94860.19271100.13613164X-RAY DIFFRACTION100
3.9486-4.51960.16292200.11663076X-RAY DIFFRACTION100
4.5196-5.69250.19761100.12943241X-RAY DIFFRACTION100
5.6925-46.23350.18422200.15243282X-RAY DIFFRACTION100

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