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- PDB-3lvk: Crystal Structure of E.coli IscS-TusA complex (form 2) -

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Basic information

Entry
Database: PDB / ID: 3lvk
TitleCrystal Structure of E.coli IscS-TusA complex (form 2)
Components
  • Cysteine desulfurase
  • Sulfurtransferase tusA
KeywordsTRANSFERASE / protein-protein complex / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / tRNA thiolation / sulfur transfer
Function / homology
Function and homology information


sulfur carrier activity / tRNA wobble position uridine thiolation / cysteine desulfurase / cysteine desulfurase activity / [2Fe-2S] cluster assembly / tRNA processing / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / metal ion binding / cytoplasm
Similarity search - Function
Sulfur carrier protein TusA / TusA-like domain / Uncharacterized protein family UPF0033 signature. / TusA-like domain / Sulfurtransferase TusA / TusA-like domain superfamily / Cysteine desulfurase IscS / Cysteine desulfurase / Translation Initiation Factor IF3 / Aminotransferase class-V, pyridoxal-phosphate binding site ...Sulfur carrier protein TusA / TusA-like domain / Uncharacterized protein family UPF0033 signature. / TusA-like domain / Sulfurtransferase TusA / TusA-like domain superfamily / Cysteine desulfurase IscS / Cysteine desulfurase / Translation Initiation Factor IF3 / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / 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, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase IscS / Sulfur carrier protein TusA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.442 Å
AuthorsShi, R. / Proteau, A. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Plos Biol. / Year: 2010
Title: Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions.
Authors: Shi, R. / Proteau, A. / Villarroya, M. / Moukadiri, I. / Zhang, L. / Trempe, J.F. / Matte, A. / Armengod, M.E. / Cygler, M.
History
DepositionFeb 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase
B: Sulfurtransferase tusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6933
Polymers56,4452
Non-polymers2471
Water82946
1
A: Cysteine desulfurase
B: Sulfurtransferase tusA
hetero molecules

A: Cysteine desulfurase
B: Sulfurtransferase tusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3856
Polymers112,8914
Non-polymers4942
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8830 Å2
ΔGint-53 kcal/mol
Surface area34690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.893, 131.407, 106.411
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cysteine desulfurase


Mass: 47326.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: iscS / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6B9, cysteine desulfurase
#2: Protein Sulfurtransferase tusA


Mass: 9118.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: tusA / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A892, Transferases; Transferring sulfur-containing groups; Sulfurtransferases
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.12M Magnisum Formate, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.442→50 Å / Num. obs: 17507 / % possible obs: 91.3 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.077 / Χ2: 0.999 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.442-2.545.20.38510920.97658.3
2.54-2.645.70.34813651.00272.6
2.64-2.766.40.33816190.99785.3
2.76-2.97.50.318581.00397.6
2.9-3.098.50.2518920.991100
3.09-3.328.70.16219191.003100
3.32-3.668.60.10119041.003100
3.66-4.198.60.07519241.002100
4.19-5.288.50.05519470.999100
5.28-507.90.03919871.00297.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P3W and 1DCJ

1p3w

1dcj


Resolution: 2.442→41.348 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.32 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 883 5.06 %
Rwork0.207 --
obs0.209 17452 90.25 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.097 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 193.04 Å2 / Biso mean: 82.174 Å2 / Biso min: 33.12 Å2
Baniso -1Baniso -2Baniso -3
1--12.637 Å20 Å2-0 Å2
2--27.952 Å20 Å2
3----15.314 Å2
Refinement stepCycle: LAST / Resolution: 2.442→41.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3619 0 15 46 3680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073700
X-RAY DIFFRACTIONf_angle_d1.014997
X-RAY DIFFRACTIONf_chiral_restr0.073556
X-RAY DIFFRACTIONf_plane_restr0.004650
X-RAY DIFFRACTIONf_dihedral_angle_d19.6151385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.442-2.5950.3241200.2681778189860
2.595-2.7960.3261430.2662525266884
2.796-3.0770.3141540.2723002315699
3.077-3.5220.2641680.24330423210100
3.522-4.4360.2451510.18430813232100
4.436-41.3540.191470.1723141328898
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)
12.8818-0.26161.72252.0951-0.04294.3631-0.47490.62860.235-0.0896-0.0809-0.0859-0.53651.07110.00020.4254-0.1686-0.06450.5410.15360.453412.0429-25.173321.4371
21.92140.02430.70892.29910.57771.5427-0.67070.09190.41930.08190.15230.2136-0.70050.6823-0.00020.8951-0.282-0.29190.74410.18750.656226.5029-14.896345.427
30.3859-0.2161-0.29640.32810.40660.4732-0.52881.53120.2198-0.2692-0.03070.0268-1.5240.5516-0.00021.0334-0.2643-0.34791.50340.31120.80762.3603-16.8735-5.6226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 12:263)A12 - 263
2X-RAY DIFFRACTION2(chain A and resid 1:11) or (chain A and resid 264:392)A1 - 11
3X-RAY DIFFRACTION2(chain A and resid 1:11) or (chain A and resid 264:392)A264 - 392
4X-RAY DIFFRACTION3(chain B and resid 4:79)B4 - 79

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