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- PDB-3wco: Crystal structure of the depentamerized mutant of N-terminal trun... -

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Basic information

Entry
Database: PDB / ID: 3wco
TitleCrystal structure of the depentamerized mutant of N-terminal truncated selenocysteine synthase SelA
ComponentsL-seryl-tRNA(Sec) selenium transferase
KeywordsTRANSFERASE / Fold-type-I pyridoxal 5'-phosphate (PLP) dependent enzyme / homodimer / 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 - #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
THIOSULFATE / L-seryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.1Apr 30, 2014Group: Database references
Revision 1.2Nov 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 1.3Dec 6, 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: L-seryl-tRNA(Sec) selenium transferase
B: L-seryl-tRNA(Sec) selenium transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5087
Polymers88,9472
Non-polymers5615
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-36 kcal/mol
Surface area30740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.190, 81.286, 95.537
Angle α, β, γ (deg.)90.000, 92.230, 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: 44473.449 Da / Num. of mol.: 2 / Fragment: UNP residues 62-452 / Mutation: 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: pET22b / 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.: 5 / Source method: obtained synthetically / Formula: O3S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM sodium MES-HCl, 2.5% PEG4000, 150mM Na2S2O3, 70mM NaNO3, pH 6.5, 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: 2.4→50 Å / Num. all: 35599 / Num. obs: 35457 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 49.31 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 15.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3520 / Rsym value: 0.561 / % 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: 2.4→41.161 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8229 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 24.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1770 5.01 %Random
Rwork0.1788 ---
obs0.1813 35363 99.14 %-
all-35670 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.3 Å2 / Biso mean: 64.5454 Å2 / Biso min: 25.91 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6048 0 25 105 6178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086146
X-RAY DIFFRACTIONf_angle_d1.1478265
X-RAY DIFFRACTIONf_chiral_restr0.07952
X-RAY DIFFRACTIONf_plane_restr0.0041043
X-RAY DIFFRACTIONf_dihedral_angle_d14.9962393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.46180.2891410.23232500264197
2.4618-2.53430.2861300.22192560269099
2.5343-2.6160.31011400.22592579271999
2.616-2.70950.32471350.219225902725100
2.7095-2.8180.29091360.215925792715100
2.818-2.94620.2851310.202825842715100
2.9462-3.10150.23691430.190425832726100
3.1015-3.29570.28221340.193726172751100
3.2957-3.55010.24481290.190526012730100
3.5501-3.90710.23011370.169826022739100
3.9071-4.47180.21461280.158426132741100
4.4718-5.63180.19661470.15642600274799
5.6318-41.16660.17031390.16362585272496
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)
12.82191.40850.06832.51480.75860.88670.0962-0.42040.02710.1578-0.07750.178-0.0372-0.111-0.02990.25010.0677-0.00960.48240.03670.283311.2802-21.259532.969
21.23560.02740.01043.24391.23792.934-0.08560.2389-0.386-0.90580.18740.0388-0.0338-0.0874-0.10030.5945-0.0163-0.00120.3105-0.02190.409918.4325-31.64896.9291
31.6113-0.0931-1.21082.45870.76693.6928-0.16770.0462-0.5818-0.55640.2196-0.13640.6707-0.0515-0.0620.6856-0.01540.00230.3485-0.02880.572221.3876-43.03679.1914
42.28920.0328-0.27853.25020.85453.4762-0.04230.0381-0.5299-0.41940.199-0.26810.48060.0107-0.10430.38480.0469-0.03030.2601-0.03690.383122.2516-34.86616.1645
51.4540.3250.02593.70980.08682.1956-0.0044-0.1604-0.2331-0.10170.0927-0.2995-0.21060.1009-0.09720.28320.0630.00920.3781-0.03060.322622.1599-22.3823.3114
65.51210.571-0.08523.3252-1.3180.8838-0.3753-0.5261-0.33670.82190.1559-0.1390.0032-0.0525-0.03070.51050.0831-0.00740.50920.13390.556217.1451-38.095634.9658
76.8553-1.5535-1.60262.3775-0.20683.2023-0.3647-0.1507-0.61930.2827-0.09360.40770.5081-0.33440.05490.60750.02950.07620.8060.34260.70850.3789-46.185843.6841
83.46530.1513-1.28262.12240.29112.6262-0.07230.0381-0.5759-0.08880.12130.4510.3981-0.64770.06340.5044-0.0446-0.03080.65240.22080.8615-3.6262-44.473733.5339
95.990.52140.10294.411-0.053.0051-0.0352-0.7343-0.26750.08170.1540.8111-0.0405-0.93770.08030.34330.0491-0.03610.76730.18460.7817-13.314-30.709834.9721
104.5949-1.3071-0.48323.0920.29872.8912-0.2347-0.8006-0.49840.10550.10350.40690.0616-0.46440.03230.4311-0.05070.02770.72280.24260.7438-5.9403-36.704338.8997
112.63741.53980.2782.76690.12541.09080.0056-0.4747-0.01110.02440.03060.22520.0551-0.1874-0.05120.31470.09340.02740.46390.03180.302713.868-17.270230.38
121.99450.33840.05592.9124-0.86393.2673-0.06830.20790.204-0.94850.02060.2444-0.05750.0781-0.0060.64660.0014-0.08960.28910.0210.40512.5304-7.31828.0655
133.24530.15770.57932.1621-1.10432.3849-0.04180.35950.6538-0.8501-0.00640.201-0.17310.13680.06370.95080.0084-0.06270.44170.06390.639614.15084.1983-1.1896
142.3149-0.24331.04372.2219-1.32862.85230.02120.07390.6477-0.49050.22610.5941-0.71240.02560.01390.70710.0619-0.12090.33140.02640.68337.84955.29599.8047
152.2185-0.22530.12062.9641-0.47672.9276-0.0324-0.24180.4316-0.41730.1290.5905-0.2205-0.1066-0.06610.37010.0647-0.05440.3523-0.01370.42767.5276-7.201218.8006
163.95880.03362.02731.51841.10631.7496-0.1193-0.97160.6320.1605-0.01260.2033-0.2253-0.27190.09540.48660.10.07570.6785-0.260.556821.12913.993339.4832
173.4972-0.21741.06242.70590.84531.92830.0058-0.47630.60730.01120.156-0.366-0.27480.1396-0.08270.38740.00640.07190.4948-0.15810.459337.03520.314835.8557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 111 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 217 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 225 through 259 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 260 through 307 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 308 through 332 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 333 through 348 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 349 through 362 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 363 through 399 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 400 through 420 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 421 through 452 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 63 through 123 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 124 through 189 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 190 through 217 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 226 through 259 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 260 through 332 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 333 through 363 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 364 through 452 )B0

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