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- PDB-3lvl: Crystal Structure of E.coli IscS-IscU complex -

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Basic information

Entry
Database: PDB / ID: 3lvl
TitleCrystal Structure of E.coli IscS-IscU complex
Components
  • Cysteine desulfurase
  • NifU-like protein
KeywordsTRANSFERASE / protein-protein complex / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Fe-S cluster assembly / sulfur transfer
Function / homology
Function and homology information


L-cysteine desulfurase complex / cysteine desulfurase / cysteine desulfurase activity / [2Fe-2S] cluster assembly / tRNA processing / iron-sulfur cluster assembly / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / iron ion binding ...L-cysteine desulfurase complex / cysteine desulfurase / cysteine desulfurase activity / [2Fe-2S] cluster assembly / tRNA processing / iron-sulfur cluster assembly / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / iron ion binding / metal ion binding / cytoplasm
Similarity search - Function
Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / ISC system FeS cluster assembly, IscU scaffold / Cysteine desulfurase IscS / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain ...Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / ISC system FeS cluster assembly, IscU scaffold / Cysteine desulfurase IscS / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Cysteine desulfurase / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase IscS / Iron-sulfur cluster assembly scaffold protein IscU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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

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Assembly

Deposited unit
B: Cysteine desulfurase
A: NifU-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4533
Polymers61,2052
Non-polymers2471
Water23413
1
B: Cysteine desulfurase
A: NifU-like protein
hetero molecules

B: Cysteine desulfurase
A: NifU-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,9056
Polymers122,4114
Non-polymers4942
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area8690 Å2
ΔGint-49 kcal/mol
Surface area38590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.647, 77.647, 355.986
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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 NifU-like protein


Mass: 13878.507 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: iscU / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ACD6
#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.: 13 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 16% PEG 8000, 0.2M Sodium Nitrate, 4% Glycerol, 0.1M Bicine pH 9.0, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 11488 / % possible obs: 83.4 % / Redundancy: 16.6 % / Rmerge(I) obs: 0.093 / Χ2: 0.997 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.1160.2854860.84936.5
3.11-3.2390.236520.96349.8
3.23-3.3811.80.1848581.00263.9
3.38-3.5613.50.1491161187.4
3.56-3.7816.70.13813060.99898.3
3.78-4.0718.50.12213581.00198.8
4.07-4.4819.50.10413421.00198.8
4.48-5.13200.0913751.00298.8
5.13-6.4619.50.0871417199
6.46-50180.0531533196.8

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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 2Z7E

1p3w

2z7e


Resolution: 3→44.489 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.269 555 4.84 %
Rwork0.225 --
obs0.227 11472 83.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.069 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso max: 124.84 Å2 / Biso mean: 65.786 Å2 / Biso min: 45.22 Å2
Baniso -1Baniso -2Baniso -3
1-17.556 Å20 Å2-0 Å2
2--17.556 Å20 Å2
3----35.111 Å2
Refinement stepCycle: LAST / Resolution: 3→44.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 15 13 3966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044018
X-RAY DIFFRACTIONf_angle_d0.6545427
X-RAY DIFFRACTIONf_chiral_restr0.047604
X-RAY DIFFRACTIONf_plane_restr0.002711
X-RAY DIFFRACTIONf_dihedral_angle_d17.2421478
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.3010.32870.3011451153847
3.301-3.7790.3041450.2422777292288
3.779-4.760.2291540.2063215336999
4.76-44.4940.2671690.2153474364399
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)
14.13370.43260.56433.5228-0.27512.68770.1439-0.26650.12960.5057-0.2098-0.4361-0.67360.1245-01.0780.18670.02740.7388-0.03050.7516-36.746443.72527.3884
22.32361.0630.49724.46131.46083.13060.0195-0.01280.1242-0.23860.02540.061-0.556-0.1933-0.00020.91850.3358-0.01060.810.02980.6503-41.927432.409-0.0167
31.63140.5604-0.36351.5672-0.06521.8535-0.14690.1634-0.0295-0.14620.1119-0.0227-0.119-0.4323-00.53160.0268-0.02920.6924-0.03230.5633-32.32966.5784-11.1826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:126)A2 - 126
2X-RAY DIFFRACTION2(chain B and resid 1:11) or (chain B and resid 264:393)B1 - 11
3X-RAY DIFFRACTION2(chain B and resid 1:11) or (chain B and resid 264:393)B264 - 393
4X-RAY DIFFRACTION3(chain B and resid 12:263)B12 - 263

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