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- PDB-3wcn: Crystal structure of the depentamerized mutant of selenocysteine ... -

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Basic information

Entry
Database: PDB / ID: 3wcn
TitleCrystal structure of the depentamerized mutant of selenocysteine synthase SelA
ComponentsL-seryl-tRNA(Sec) selenium transferase
KeywordsTRANSFERASE / Fold-type-I pyridoxal 5'-phosphate (PLP) dependent enzyme / L-seryl-tRNA(Sec) selenium transferase / selenocysteine synthesis / selenium metabolism
Function / homology
Function and homology information


L-seryl-tRNASec selenium transferase / L-seryl-tRNA(Sec) selenium transferase activity / conversion of seryl-tRNAsec to selenocys-tRNAsec / selenocysteine incorporation / identical protein binding / cytoplasm
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #110 / L-seryl-tRNA(Sec) selenium transferase / L-seryl-tRNA selenium transferase-like / L-seryl-tRNA selenium transferase / 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 / Alpha-Beta Complex ...Aspartate Aminotransferase, domain 1 - #110 / L-seryl-tRNA(Sec) selenium transferase / L-seryl-tRNA selenium transferase-like / L-seryl-tRNA selenium transferase / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOSULFATE / L-seryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsItoh, Y. / Sekine, S. / Yokoyama, S.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Dimer-Dimer Interaction of the Bacterial Selenocysteine Synthase SelA Promotes Functional Active-Site Formation and Catalytic Specificity
Authors: Itoh, Y. / Brocker, M.J. / Sekine, S. / Soll, D. / Yokoyama, S.
History
DepositionMay 29, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Apr 30, 2014Group: Database references
Revision 1.3Nov 8, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-seryl-tRNA(Sec) selenium transferase
B: L-seryl-tRNA(Sec) selenium transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7936
Polymers102,3452
Non-polymers4494
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9300 Å2
ΔGint-37 kcal/mol
Surface area39790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.137, 144.137, 273.406
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein L-seryl-tRNA(Sec) selenium transferase / Selenocysteine synthase / Sec synthase / Selenocysteinyl-tRNA(Sec) synthase


Mass: 51172.387 Da / Num. of mol.: 2
Mutation: K19A, K21A, K46A, K48A, T191Y, T192Y, D199R, Y220P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1031, selA / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)
References: UniProt: O67140, L-seryl-tRNASec selenium transferase
#2: Chemical
ChemComp-THJ / THIOSULFATE


Mass: 112.128 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O3S2
Has protein modificationY

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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: 3.47 Å3/Da / Density % sol: 64.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100mM trisodium citrate-HCl, 580-590mM trisodium citrate, 100mM L-serine, 100mM Na2S2O3, pH 6, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2008 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. all: 21159 / Num. obs: 21096 / % possible obs: 99.7 % / Observed criterion σ(I): -2 / Redundancy: 6 % / Biso Wilson estimate: 120.57 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 17.2
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 2.75 / Num. unique all: 2066 / Rsym value: 0.712 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W1I

3w1i


Resolution: 3.35→47.321 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7957 / SU ML: 0.34 / σ(F): 1.35 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1062 5.05 %Random
Rwork0.1905 ---
obs0.1928 21028 99.25 %-
all-21182 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 473.48 Å2 / Biso mean: 151.3732 Å2 / Biso min: 70.47 Å2
Refinement stepCycle: LAST / Resolution: 3.35→47.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7035 0 20 0 7055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017142
X-RAY DIFFRACTIONf_angle_d1.2739596
X-RAY DIFFRACTIONf_chiral_restr0.0751107
X-RAY DIFFRACTIONf_plane_restr0.0061218
X-RAY DIFFRACTIONf_dihedral_angle_d15.6362805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.348-3.50040.3151240.26312435255999
3.5004-3.68490.30361360.23372454259099
3.6849-3.91570.27241370.225224632600100
3.9157-4.21780.23721390.183724602599100
4.2178-4.6420.23681280.155824852613100
4.642-5.31290.21731360.157125092645100
5.3129-6.69070.22711340.217825342668100
6.6907-47.32530.2281280.18552626275497
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)
13.5741-0.27790.33043.0092-2.4923.87010.4750.29210.5193-1.02710.09340.3086-0.460.57720.1781.31640.0540.0091.0401-0.1461.6005-31.0538-22.3391-58.6616
22.0573-0.75160.24012.0061-0.520.116-0.2201-0.60520.1773-0.26410.25620.53940.15250.0436-0.05890.94790.2759-0.09671.1864-0.22031.2214-34.3344-41.1284-44.1774
32.3218-1.8637-1.8175.21481.15482.66840.0588-0.4261-0.1046-0.14540.01390.31370.189-0.4961-0.08380.6640.0163-0.02711.0730.07830.7811-19.0547-72.4196-43.4897
41.5225-0.9275-0.62723.003-0.10520.55690.0798-0.47340.1830.46430.17410.874-0.3113-0.7059-0.18870.99520.13880.1551.7728-0.01111.2192-37.9499-57.6619-32.0681
51.5458-1.5535-0.84895.4176-1.86292.970.3349-0.5973-0.3466-0.76780.42081.8887-0.1285-0.4781-0.46861.16580.2167-0.17881.97960.03981.8904-49.8008-50.711-41.8852
65.2791-0.0842-0.50326.5948-1.32243.78590.19080.2751-1.13490.90341.0272-0.57491.73490.9822-0.85511.73620.3876-0.26112.2278-0.53181.4089-15.2577-75.5903-9.7234
70.92381.82860.31362.16680.66352.0734-0.102-0.4712-0.25650.68760.2206-0.67780.27850.4174-0.211.18680.4-0.06571.8904-0.45341.2419-12.9711-54.8634-20.7013
84.2096-0.9394-1.57182.7076-0.30343.89360.1296-0.15760.9217-0.0903-0.1082-0.399-0.31560.34220.0340.84040.0351-0.02250.8703-0.10711.1035-6.9677-44.6341-54.021
90.9950.3468-0.17452.54780.14523.3141-0.0106-0.65870.68691.37010.0235-0.1762-0.53990.8959-0.08961.4821-0.0094-0.12681.6168-0.44411.3303-10.27-36.1099-29.9864
101.7471-0.4205-0.59933.6582-3.1654.48730.0864-0.58320.26591.446-0.0882-0.7858-0.46081.0809-0.06331.72910.1816-0.42041.9724-0.48331.52190.1422-41.8877-18.1363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 43 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 102 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 307 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 308 through 378 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 379 through 452 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 43 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 44 through 102 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 103 through 307 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 308 through 378 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 379 through 452 )B0

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