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- PDB-3w1h: Crystal structure of the selenocysteine synthase SelA from Aquife... -

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Basic information

Entry
Database: PDB / ID: 3w1h
TitleCrystal structure of the selenocysteine synthase SelA from Aquifex aeolicus
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 - #110 / 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 ...Aspartate Aminotransferase, domain 1 - #110 / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.893 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 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
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
Revision 1.2Dec 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
C: L-seryl-tRNA(Sec) selenium transferase
D: L-seryl-tRNA(Sec) selenium transferase
E: L-seryl-tRNA(Sec) selenium transferase


Theoretical massNumber of molelcules
Total (without water)254,6265
Polymers254,6265
Non-polymers00
Water00
1
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

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


Theoretical massNumber of molelcules
Total (without water)509,25210
Polymers509,25210
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area50550 Å2
ΔGint-155 kcal/mol
Surface area168710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.033, 167.033, 211.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 50925.160 Da / Num. of mol.: 5 / Mutation: K19A, K21A, K46A, K48A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: selA / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)
References: UniProt: O67140, L-seryl-tRNASec selenium transferase

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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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 120mM Tris-HCl, 11% PEG 4000, 200mM MgCl2, 90mM 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

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2007 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.893→50 Å / Num. all: 28051 / Num. obs: 26396 / % possible obs: 94.1 % / Observed criterion σ(I): -2 / Redundancy: 9.1 % / Biso Wilson estimate: 130.32 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 15.3
Reflection shellResolution: 3.9→4.04 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 2.02 / Num. unique all: 2717 / Rsym value: 0.736 / % possible all: 86.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3w1i


Resolution: 3.893→49.247 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7564 / SU ML: 1.35 / σ(F): 1.35 / Phase error: 30.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 1345 5.1 %RANDOM
Rwork0.2203 ---
obs0.2235 26354 94.11 %-
all-28003 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 146.016 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso max: 411.5 Å2 / Biso mean: 209.7605 Å2 / Biso min: 104.6 Å2
Baniso -1Baniso -2Baniso -3
1--46.8339 Å2-0 Å20 Å2
2---46.8339 Å20 Å2
3---93.6677 Å2
Refinement stepCycle: LAST / Resolution: 3.893→49.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16913 0 0 0 16913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817138
X-RAY DIFFRACTIONf_angle_d1.22223043
X-RAY DIFFRACTIONf_chiral_restr0.072657
X-RAY DIFFRACTIONf_plane_restr0.0042929
X-RAY DIFFRACTIONf_dihedral_angle_d13.556690
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8931-4.03220.41180.36862244236287
4.0322-4.19350.35351130.31272340245389
4.1935-4.38430.29891200.27282400252091
4.3843-4.61520.29161490.21832388253792
4.6152-4.90420.25151380.19572485262395
4.9042-5.28240.2871430.19322544268796
5.2824-5.81320.26811340.22892583271798
5.8132-6.65270.32661520.25012607275998
6.6527-8.3750.26611330.1972668280198
8.375-49.25050.25151450.18792750289596
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)
15.05821.8287-3.0924.1397-2.35595.13841.2473-1.16720.08291.8063-0.2255-1.0949-1.58170.3846-1.16772.2364-0.39540.0451.7874-0.12311.906-95.85247.8492-18.4155
26.79942.4938-1.20184.0433-1.08041.7269-0.25631.69740.7919-0.07010.03840.36070.04510.04670.28961.42710.16860.13741.81940.30360.9649-75.823146.488-60.2215
37.1439-0.671-1.83792.3936-1.28333.35120.9537-0.09282.87671.1937-0.1770.2385-1.7519-0.9466-0.63212.06010.21640.52421.5753-0.11652.7163-94.794568.4339-41.1396
44.3177-0.3261-4.20692.5786-0.05691.81920.51362.8141-0.2546-1.3314-0.7938-0.13630.1529-2.10660.41242.1890.28010.26143.0567-0.22822.2156-96.877732.8696-72.4148
53.825-1.43551.03626.4641-1.0065-0.3904-0.3429-0.28730.00160.81180.45250.6820.23950.0598-0.1031.7472-0.03860.34471.59930.05490.6497-76.256529.4428-36.6651
63.7032-0.01682.17132.94440.29942.1760.03130.6439-0.6564-0.73170.326-0.39640.2495-0.7444-0.33611.8501-0.16240.55731.9386-0.38241.6444-104.874515.6644-50.8351
75.9888-0.64242.9572.5488-1.35992.08480.1288-2.4712-0.91451.2241.5791-0.1915-1.0075-1.4851-1.59382.16440.28450.27082.37160.0651.5844-60.8554-24.9713-12.8545
84.3714-2.53961.2247.2335-1.87810.65480.5050.4568-0.6989-0.6541-0.57480.9705-0.0541-0.19520.05991.34870.00250.07541.6566-0.16050.8933-61.3088-7.1263-55.637
93.28950.6054-0.06752.5693-1.82251.59220.3084-1.0722-0.15490.55340.4870.0665-0.2584-0.5294-0.6821.92370.03510.62251.9370.21491.9878-84.1068-18.2203-32.1173
105.2346-1.16210.97674.5256-1.59284.04630.1947-0.2389-2.4381-1.01131.0468-0.76170.8941-0.1933-1.2292.25640.1321-0.32121.491-0.22132.7492-51.5166-34.0681-54.9068
116.00640.74561.44492.63890.55650.44590.1428-0.761-0.28940.8124-0.4258-0.47020.1970.14820.2661.8594-0.0241-0.06961.30970.28651.053-41.0592-13.8168-35.8009
124.10182.12942.27385.31840.14433.04631.23940.9966-0.8164-0.1415-0.7714-1.07931.25740.4296-0.20412.07030.2369-0.10861.95880.0092.5379-40.2455-44.8089-51.3743
135.00040.91890.23072.97790.78043.7406-0.0885-0.5163-1.45850.4902-0.23512.0866-0.58651.0358-0.21232.2881-0.2557-0.14481.71330.62044.59418.9766-23.0826-37.1394
147.56770.56141.30244.7190.57191.6244-0.07411.5423-1.9585-0.57840.1979-1.82080.48060.2724-0.08121.24430.02020.16011.3861-0.56992.5236-5.5256-10.554-61.876
154.1024-3.25552.45312.32890.72492.72931.614-0.5574-1.61911.47830.11010.30991.7393-0.0914-1.76182.6189-0.2674-0.78581.64020.47453.96662.3807-36.8195-40.6171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:89)A1 - 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 10:89)B10 - 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 1:89)C1 - 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 58:89)D58 - 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 54:89)E54 - 89
14X-RAY DIFFRACTION14CHAIN E AND (RESSEQ 90:338)E90 - 338
15X-RAY DIFFRACTION15CHAIN E AND (RESSEQ 339:452)E339 - 452

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