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- PDB-3lvj: Crystal Structure of E.coli IscS-TusA complex (form 1) -

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Basic information

Entry
Database: PDB / ID: 3lvj
TitleCrystal Structure of E.coli IscS-TusA complex (form 1)
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: 2.435 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: Cysteine desulfurase
C: Sulfurtransferase tusA
D: Sulfurtransferase tusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3856
Polymers112,8914
Non-polymers4942
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-51 kcal/mol
Surface area34660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.299, 106.545, 122.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cysteine desulfurase


Mass: 47326.879 Da / Num. of mol.: 2
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 / tRNA 2-thiouridine synthesizing protein A


Mass: 9118.479 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.08 Å3/Da / Density % sol: 40.95 %
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: 2.435→50 Å / Num. obs: 34585 / % possible obs: 96.4 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.072 / Χ2: 1.004 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.45-2.542.80.36527820.96879
2.54-2.643.40.34131351.01989.2
2.64-2.764.30.30334040.99396.2
2.76-2.95.40.25735381.03499.3
2.9-3.096.40.21435291.01299.9
3.09-3.3270.14335881100
3.32-3.667.30.08635631.004100
3.66-4.197.40.05836051.001100
4.19-5.287.30.04536380.995100
5.28-506.90.03238031.00299.6

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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: 2.435→46.646 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 1722 5 %
Rwork0.222 --
obs0.223 34434 95.55 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.555 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 132.53 Å2 / Biso mean: 49.007 Å2 / Biso min: 24.11 Å2
Baniso -1Baniso -2Baniso -3
1--7.777 Å2-0 Å20 Å2
2---7.554 Å2-0 Å2
3---15.331 Å2
Refinement stepCycle: LAST / Resolution: 2.435→46.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7205 0 30 213 7448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047365
X-RAY DIFFRACTIONf_angle_d0.6759947
X-RAY DIFFRACTIONf_chiral_restr0.051108
X-RAY DIFFRACTIONf_plane_restr0.0021294
X-RAY DIFFRACTIONf_dihedral_angle_d17.2442747
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 (%)
2.435-2.5220.3621180.2892508262674
2.522-2.6230.3021600.2882971313188
2.623-2.7430.3021760.2743235341196
2.743-2.8870.2791700.2583370354099
2.887-3.0680.2881680.25333873555100
3.068-3.3050.3041700.24534093579100
3.305-3.6370.2361700.21334013571100
3.637-4.1630.2011940.18934183612100
4.163-5.2440.1932100.18234383648100
5.244-46.6550.1961860.1973575376199
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)
11.66830.4622-0.36881.40570.04851.4294-0.1457-0.0670.1447-0.14990.02570.1697-0.0510.033500.22760.0012-0.0170.2578-0.04760.253-8.5575.161-7.1809
22.57650.67580.61521.78651.01252.87230.0202-0.1035-0.24850.0462-0.0087-0.06250.4696-0.051900.4201-0.00670.02450.2681-0.02210.3501-23.2722-18.1088-17.6952
31.8740.25430.2441.4911-0.16661.3403-0.148-0.1059-0.3666-0.14630.0066-0.32780.0895-0.0314-00.25680.01580.09290.27570.03860.366815.4383-5.1035-7.5251
42.53720.8819-0.13462.1794-0.07363.3873-0.153-0.02260.0015-0.10450.0482-0.1099-0.28890.0385-00.3607-0.01220.03250.2889-0.00120.303929.876518.7212-18.0019
50.95860.3642-0.30350.81640.65930.7011-0.1943-0.09330.6229-0.91450.32140.2383-0.29880.02940.00010.6386-0.1672-0.13770.4564-0.00380.68170.906832.0992-15.5335
60.65940.32490.07990.6222-0.4730.3427-0.0895-0.0516-0.213-1.37660.36260.01770.045-0.12670.00010.8726-0.10510.05630.4899-0.03070.70395.8808-32.0707-15.484
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 264:390)A1 - 11
3X-RAY DIFFRACTION2(chain A and resid 1:11) or (chain A and resid 264:390)A264 - 390
4X-RAY DIFFRACTION3(chain B and resid 12:263)B12 - 263
5X-RAY DIFFRACTION4(chain B and resid 1:11) or (chain B and resid 264:392)B1 - 11
6X-RAY DIFFRACTION4(chain B and resid 1:11) or (chain B and resid 264:392)B264 - 392
7X-RAY DIFFRACTION5(chain C and resid 4:80)C4 - 80
8X-RAY DIFFRACTION6(chain D and resid 4:80)D4 - 80

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