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- PDB-1p3w: X-ray crystal structure of E. coli IscS -

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Basic information

Entry
Database: PDB / ID: 1p3w
TitleX-ray crystal structure of E. coli IscS
ComponentsCysteine desulfurase
KeywordsLYASE / iron sulfur cluster / Nifs / CsdB
Function / homology
Function and homology information


IscS-TusA complex / oxazole or thiazole biosynthetic process / IscS-IscU complex / tRNA 4-thiouridine biosynthesis / sulfur compound transport / sulfurtransferase complex / selenocysteine catabolic process / sulfur carrier activity / tRNA wobble position uridine thiolation / detection of UV ...IscS-TusA complex / oxazole or thiazole biosynthetic process / IscS-IscU complex / tRNA 4-thiouridine biosynthesis / sulfur compound transport / sulfurtransferase complex / selenocysteine catabolic process / sulfur carrier activity / tRNA wobble position uridine thiolation / detection of UV / L-cysteine desulfurase complex / selenocysteine lyase activity / cysteine desulfurase / cysteine desulfurase activity / L-cysteine catabolic process / thiamine biosynthetic process / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / metal ion binding / cytosol
Similarity search - Function
Cysteine desulfurase IscS / 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) ...Cysteine desulfurase IscS / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCupp-Vickery, J.R. / Vickery, L.E. / Urbina, H.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of IscS, a Cysteine Desulfurase from Escherichia coli
Authors: Cupp-Vickery, J.R. / Urbina, H. / Vickery, L.E.
History
DepositionApr 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Apr 3, 2024Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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
B: Cysteine desulfurase
A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7934
Polymers90,2992
Non-polymers4942
Water11,259625
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-26 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.709, 101.974, 108.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological unit is a dimer.

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Components

#1: Protein Cysteine desulfurase / / ThiI transpersulfidase / NifS protein homolog


Mass: 45149.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ISCS OR B2530 OR C3056 OR Z3797 OR ECS3396 OR SF2577 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6B7, Lyases; Carbon-sulfur lyases
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 2.19 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 295.1 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 22.1K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 %(w/v)PEG100001reservoir
220 %(w/v)PEG20001reservoir
30.1 MTris-HCl1reservoirpH9.
470 mMsodium citrate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 46748 / Num. obs: 46748 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.068 / Net I/σ(I): 7.1
Reflection shellResolution: 2.1→2.27 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3435 / Rsym value: 0.245 / % possible all: 93.3
Reflection
*PLUS
Lowest resolution: 500 Å / % possible obs: 96.9 % / Num. measured all: 146645 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
Lowest resolution: 2.15 Å / % possible obs: 93.3 % / Rmerge(I) obs: 0.245

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T.m. Nifs

Resolution: 2.1→5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 4694 10 %random
Rwork0.206 ---
obs0.206 46748 97 %-
Refinement stepCycle: LAST / Resolution: 2.1→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5988 0 30 625 6643
LS refinement shellResolution: 2.1→2.11 Å
RfactorNum. reflection% reflection
Rfree0.261 85 -
Rwork0.244 --
obs-772 93.3 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0058
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.39
LS refinement shell
*PLUS
Highest resolution: 2.1 Å

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