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- PDB-3w1i: Crystal structure of the N-terminal truncated selenocysteine synt... -

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Basic information

Entry
Database: PDB / ID: 3w1i
TitleCrystal structure of the N-terminal truncated selenocysteine synthase SelA
ComponentsL-seryl-tRNA(Sec) selenium transferase
KeywordsTRANSFERASE / homodecamer / pentamer of dimers / 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 / selenocysteine incorporation / identical protein binding / cytoplasm
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #180 / 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 - #180 / 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
: / : / L-seryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.192 Å
AuthorsItoh, Y. / Sekine, S. / Yokoyama, S.
CitationJournal: Science / Year: 2013
Title: Decameric SelA-tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation
Authors: Itoh, Y. / Brocker, M.J. / Sekine, S. / Hammond, G. / Suetsugu, S. / Soll, D. / Yokoyama, S.
History
DepositionNov 15, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

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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
C: L-seryl-tRNA(Sec) selenium transferase
D: L-seryl-tRNA(Sec) selenium transferase
E: L-seryl-tRNA(Sec) selenium transferase
F: L-seryl-tRNA(Sec) selenium transferase
G: L-seryl-tRNA(Sec) selenium transferase
H: L-seryl-tRNA(Sec) selenium transferase
I: L-seryl-tRNA(Sec) selenium transferase
J: L-seryl-tRNA(Sec) selenium transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)444,31817
Polymers443,73310
Non-polymers5867
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50290 Å2
ΔGint-193 kcal/mol
Surface area144270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.825, 280.936, 97.645
Angle α, β, γ (deg.)90.000, 113.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 44373.262 Da / Num. of mol.: 10
Fragment: the core and C-terminal domains, UNP residues 62-452
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: selA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)
References: UniProt: O67140, L-seryl-tRNASec selenium transferase
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6353.27
2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 120mM Tris-HCl, 11% PEG 4000, 400mM CaCl2, 160mM KCl, 5.0mM NiCl2, 50mM Na2S2O3, 50mM L-serine, 0.2M NaCl, 10mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2902
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-17A11.07117
SYNCHROTRONSPring-8 BL41XU20.97917, 0.97947
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2701CCDMar 4, 2008mirrors
ADSC QUANTUM 3152CCDFeb 19, 2008mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiSINGLE WAVELENGTHMx-ray1
2SiMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.071171
20.979171
30.979471
ReflectionResolution: 3.192→50 Å / Num. all: 75523 / Num. obs: 75145 / % possible obs: 99.5 % / Observed criterion σ(I): -2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 22.4
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.5 / Num. unique all: 7513 / Rsym value: 0.674 / % possible all: 96

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.192→48.941 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8066 / SU ML: 0.87 / σ(F): 1.35 / Phase error: 26.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 3750 5 %RANDOM
Rwork0.1738 ---
obs0.1769 75046 99.02 %-
all-75789 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 83.01 Å2 / ksol: 0.294 e/Å3
Displacement parametersBiso max: 377.04 Å2 / Biso mean: 130.1176 Å2 / Biso min: 52.49 Å2
Baniso -1Baniso -2Baniso -3
1--21.7714 Å2-0 Å2-6.6801 Å2
2---9.6703 Å20 Å2
3---31.4417 Å2
Refinement stepCycle: LAST / Resolution: 3.192→48.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30712 0 7 0 30719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931122
X-RAY DIFFRACTIONf_angle_d1.2241863
X-RAY DIFFRACTIONf_chiral_restr0.0714840
X-RAY DIFFRACTIONf_plane_restr0.0045321
X-RAY DIFFRACTIONf_dihedral_angle_d14.45912109
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1925-3.23290.36791050.27712173227882
3.2329-3.27540.33761500.2722554270496
3.2754-3.32020.33031480.28032623277199
3.3202-3.36770.36441220.263427072829100
3.3677-3.41790.31281530.258825672720100
3.4179-3.47130.28631390.232727262865100
3.4713-3.52820.32361360.23126202756100
3.5282-3.5890.30831420.2326892831100
3.589-3.65430.25761360.216426212757100
3.6543-3.72450.31541370.216327092846100
3.7245-3.80050.3051210.202726502771100
3.8005-3.88310.25481640.187426672831100
3.8831-3.97340.23071420.178326222764100
3.9734-4.07280.24561380.169327262864100
4.0728-4.18280.23741490.168726322781100
4.1828-4.30580.24531480.164826232771100
4.3058-4.44470.18761370.138826842821100
4.4447-4.60350.18471480.128726412789100
4.6035-4.78760.17641350.119526712806100
4.7876-5.00530.19741310.135426862817100
5.0053-5.26890.22671330.149226692802100
5.2689-5.59860.23851260.166526802806100
5.5986-6.03020.24061370.201126752812100
6.0302-6.63570.29171530.201426932846100
6.6357-7.59280.22911370.166626642801100
7.5928-9.55440.17811480.126326782826100
9.5544-48.9470.21041350.17562646278198
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)
14.6059-0.51071.23241.79040.81064.9792-0.07370.70790.4068-0.1332-0.1048-0.2889-0.41470.7363-0.17880.86580.04610.01270.8974-0.00750.9347-49.4175192.19199.1814
22.255-0.5647-0.515.21060.64671.4515-0.1243-0.5488-0.04240.54560.0718-0.21380.03140.03250.06040.75120.1405-0.15790.81710.03260.6458-28.5463177.2659107.3905
32.2608-0.90751.31172.0219-1.95452.5299-0.0489-0.2981-0.22790.48230.29510.23290.002-0.0178-0.27791.06440.05670.05171.0315-0.02220.6671-61.8669187.0468110.2525
48.29571.2256-0.09948.8335-0.01355.80670.0521-0.56121.43961.54510.48671.4791-0.08750.3222-0.12871.3928-0.0077-0.00560.9407-0.23721.4353-23.6462205.3251106.8689
53.53640.5121-1.69391.2783-0.42933.20360.03340.42750.37120.1773-0.0718-0.1297-0.3295-0.09440.04280.69250.1216-0.03110.70430.03450.8529-27.7683195.289484.3038
62.2884-0.0359-0.21432.3968-0.04854.38980.3229-0.6530.84020.6777-0.2629-1.1757-1.54520.9184-0.11451.7051-0.2864-0.12711.2957-0.11551.8523-18.5506219.2709107.5034
75.8765-0.45581.7376.174-1.41147.65460.17610.7229-0.32290.2920.75890.38270.01120.0447-1.02830.96740.0529-0.03630.76970.04451.188610.6886215.862761.9938
83.61341.6119-1.44021.7103-1.22173.29110.096-0.13430.321-0.0321-0.13570.2608-0.3996-0.05590.0560.72750.0726-0.08380.5937-0.00540.78515.7179197.025280.2945
91.16270.37681.57993.5908-1.49273.1315-0.43990.03870.71420.6380.34751.0343-1.3792-0.40460.14471.49610.1975-0.14530.87170.03161.37766.1182229.204972.23
104.4087-0.31030.12471.8851-0.42613.4939-0.4415-0.23580.01680.85770.5280.2109-0.3831-0.0162-0.08051.0310.1125-0.03730.95880.12180.833237.4106201.921962.8101
111.6810.8768-0.43044.4761.29081.34890.0250.66020.2886-0.949-0.03310.6783-0.2162-0.0710.00650.94260.0991-0.30160.8010.0640.729416.4863192.09751.7607
123.20181.01920.92380.82031.772.6753-0.08370.7190.1212-0.42880.4238-0.1186-0.09120.4381-0.22861.16440.04420.04841.10310.1450.932749.7347201.644753.4191
133.53330.07920.37024.71041.26436.2429-0.28111.055-0.0498-1.442-0.4267-0.7664-1.47110.66230.88511.3435-0.18930.07531.23910.19350.830740.2632156.902127.1459
142.338-0.1430.40455.61232.51983.5549-0.3486-0.21990.16920.0320.4065-0.53540.1850.581-0.04970.64610.074-0.00460.84810.02710.51838.6242154.435753.2874
153.7633-0.31411.72851.9174-1.53034.711-0.91191.37271.5247-0.8650.12520.3001-0.90430.84580.75991.809-0.4771-0.26811.41880.27711.619351.5356168.380224.1515
166.0117-2.56681.7533.8218-1.40886.8219-0.446-0.64670.3215-0.1260.033-0.9211-1.28590.27180.43691.04970.10910.03590.9501-0.04120.97746.4882131.276541.5294
176.4248-1.1806-0.74893.27051.86484.016-0.22350.484-0.2477-0.57640.03420.6340.1027-0.1980.18990.7781-0.0182-0.08020.56640.02350.648221.5778138.759835.5304
183.6055-0.36621.2512.5581.46093.85810.3154-0.2208-0.89480.93980.2348-0.66360.84360.8165-0.5121.50620.1894-0.19061.1225-0.04551.042647.902116.411732.9277
195.3056-1.89850.01523.381-0.29423.2035-0.56320.3749-1.7326-0.87060.6125-0.22360.3795-0.12580.04341.4266-0.01460.49131.058-0.42211.89560.214497.098841.764
204.03111.19560.7194.32681.26361.5990.1338-0.3976-1.36890.2045-0.1899-1.18440.31370.27390.03540.80390.01130.12090.82610.28321.45328.633107.743863.3506
211.21680.77021.42821.9560.52373.98240.0150.8266-0.467-0.70.3336-0.33210.59890.7879-0.29671.55890.00070.33731.3792-0.22282.16211.86992.246332.4844
225.74151.19471.05773.6481-0.46554.3431-0.3324-0.56-1.76520.13171.01840.31090.1152-0.2763-0.75091.1906-0.00130.29250.97920.42091.8803-10.914588.895468.4145
235.8277-1.25820.11886.6831.6361.90750.07670.0466-0.4631-0.5688-0.00140.00890.0683-0.2709-0.0740.7767-0.02220.09960.66590.15670.5677-19.7258109.7556.7484
242.6096-1.46852.18583.2482-0.94962.72030.5418-1.2664-1.65150.62010.28070.65630.4826-0.6563-0.81451.2121-0.1948-0.01291.49130.66192.1279-23.123779.560972.7434
253.891-1.48180.52693.85860.45097.0459-0.55940.6980.07390.5527-0.34562.18880.0598-0.7941.08850.8933-0.38970.13361.4598-0.19631.7718-56.5741116.744290.0895
265.91210.0876-1.34774.0115-0.75332.14640.1646-0.74280.06870.5886-0.16640.21340.30270.0807-0.01960.8053-0.11420.02130.9696-0.03220.5485-32.4998121.853497.0934
273.8481-0.43051.02880.8369-0.66060.70710.50980.1736-1.23160.0121-0.36640.57090.4491-0.3426-0.16931.4491-0.25250.02711.3992-0.27871.6148-59.4338101.271888.9366
285.6065-1.21191.59741.94731.20155.32150.5193-0.70850.25790.4673-0.21711.14130.5386-1.4733-0.26850.985-0.15780.43731.6447-0.20021.1859-51.3394135.2186113.0032
291.69960.4912-0.22194.3174-0.54231.8693-0.28780.20280.2599-0.15720.0771.05010.0782-0.84560.2210.64250.0028-0.00411.1955-0.08310.9819-50.1509143.866689.1803
302.3555-0.28551.04382.0608-1.47061.9288-0.3047-0.80810.46560.86420.2710.2625-0.1725-1.1501-0.02581.1781-0.00770.38282.0193-0.38741.5918-59.8469144.1672122.0212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 61:89)A61 - 89
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 90:338)A90 - 338
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 339:452)A339 - 452
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 65:89)B65 - 89
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 90:338)B90 - 338
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 339:452)B339 - 452
7X-RAY DIFFRACTION7CHAIN C AND (RESSEQ 61:89)C61 - 89
8X-RAY DIFFRACTION8CHAIN C AND (RESSEQ 90:338)C90 - 338
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 339:452)C339 - 452
10X-RAY DIFFRACTION10CHAIN D AND (RESSEQ 64:89)D64 - 89
11X-RAY DIFFRACTION11CHAIN D AND (RESSEQ 90:338)D90 - 338
12X-RAY DIFFRACTION12CHAIN D AND (RESSEQ 339:452)D339 - 452
13X-RAY DIFFRACTION13CHAIN E AND (RESSEQ 62:89)E62 - 89
14X-RAY DIFFRACTION14CHAIN E AND (RESSEQ 90:338)E90 - 338
15X-RAY DIFFRACTION15CHAIN E AND (RESSEQ 339:452)E339 - 452
16X-RAY DIFFRACTION16CHAIN F AND (RESSEQ 61:89)F61 - 89
17X-RAY DIFFRACTION17CHAIN F AND (RESSEQ 90:338)F90 - 338
18X-RAY DIFFRACTION18CHAIN F AND (RESSEQ 339:452)F339 - 452
19X-RAY DIFFRACTION19CHAIN G AND (RESSEQ 64:89)G64 - 89
20X-RAY DIFFRACTION20CHAIN G AND (RESSEQ 90:338)G90 - 338
21X-RAY DIFFRACTION21CHAIN G AND (RESSEQ 339:452)G339 - 452
22X-RAY DIFFRACTION22CHAIN H AND (RESSEQ 63:89)H63 - 89
23X-RAY DIFFRACTION23CHAIN H AND (RESSEQ 90:338)H90 - 338
24X-RAY DIFFRACTION24CHAIN H AND (RESSEQ 339:452)H339 - 452
25X-RAY DIFFRACTION25CHAIN I AND (RESSEQ 64:89)I64 - 89
26X-RAY DIFFRACTION26CHAIN I AND (RESSEQ 90:338)I90 - 338
27X-RAY DIFFRACTION27CHAIN I AND (RESSEQ 339:452)I339 - 452
28X-RAY DIFFRACTION28CHAIN J AND (RESSEQ 64:89)J64 - 89
29X-RAY DIFFRACTION29CHAIN J AND (RESSEQ 90:338)J90 - 338
30X-RAY DIFFRACTION30CHAIN J AND (RESSEQ 339:452)J339 - 452

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