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- PDB-5ft5: Crystal structure of the cysteine desulfurase CsdA (persulfurated... -

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Basic information

Entry
Database: PDB / ID: 5ft5
TitleCrystal structure of the cysteine desulfurase CsdA (persulfurated) from Escherichia coli at 2.384 Angstroem resolution
ComponentsL-CYSTEINE DESULFURASE CSDA
KeywordsTRANSFERASE / L-CYSTEINE DESULFURASE / SULFUR ACCEPTOR / TRANSPERSULFURATION / SULFUR TRAFFICKING
Function / homology
Function and homology information


sulfur compound transport / selenocysteine catabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / sulfur amino acid metabolic process / selenocysteine lyase / selenocysteine lyase activity / sulfurtransferase activity / L-cysteine desulfurase complex / L-cysteine catabolic process ...sulfur compound transport / selenocysteine catabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / sulfur amino acid metabolic process / selenocysteine lyase / selenocysteine lyase activity / sulfurtransferase activity / L-cysteine desulfurase complex / L-cysteine catabolic process / cysteine desulfurase / cysteine desulfurase activity / iron-sulfur cluster assembly / pyridoxal phosphate binding / hydrolase activity
Similarity search - Function
Cysteine desulphurase, catalytic subunit, CsdA / Cysteine desulfurase, SufS / 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 desulphurase, catalytic subunit, CsdA / Cysteine desulfurase, SufS / 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
DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / L(+)-TARTARIC ACID / Cysteine desulfurase CsdA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.384 Å
AuthorsFernandez, F.J. / Arda, A. / Lopez-Estepa, M. / Aranda, J. / Penya-Soler, E. / Garces, F. / Quintana, J.F. / Round, A. / Campos-Oliva, R. / Bruix, M. ...Fernandez, F.J. / Arda, A. / Lopez-Estepa, M. / Aranda, J. / Penya-Soler, E. / Garces, F. / Quintana, J.F. / Round, A. / Campos-Oliva, R. / Bruix, M. / Coll, M. / Tunon, I. / Jimenez-Barbero, J. / Vega, M.C.
CitationJournal: Acs Catalysis / Year: 2016
Title: Mechanism of Sulfur Transfer Across Protein-Protein Interfaces: The Cysteine Desulfurase Model System
Authors: Fernandez, F.J. / Arda, A. / Lopez-Estepa, M. / Aranda, J. / Penya-Soler, E. / Garces, F. / Quintana, J.F. / Round, A. / Campos-Oliva, R. / Bruix, M. / Coll, M. / Tunon, I. / Jimenez-Barbero, J. / Vega, M.C.
History
DepositionJan 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Structure summary
Category: pdbx_database_related / struct / Item: _pdbx_database_related.details / _struct.title
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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
A: L-CYSTEINE DESULFURASE CSDA
B: L-CYSTEINE DESULFURASE CSDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,43417
Polymers86,6122
Non-polymers1,82215
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10880 Å2
ΔGint-41.4 kcal/mol
Surface area27850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.347, 99.533, 141.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.79, -0.4144, -0.4518), (-0.4013, -0.2075, 0.8921), (-0.4634, 0.8861, -0.0023)
Vector: 64.2123, 45.8828, -11.5386)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein L-CYSTEINE DESULFURASE CSDA / CYSTEINE SULFINATE DESULFINASE / CSD / SELENOCYSTEINE LYASE / L-CYSTEINE DESULFURASE CSDA


Mass: 43306.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q46925, cysteine desulfurase, Lyases; Carbon-sulfur lyases, selenocysteine lyase

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Non-polymers , 5 types, 314 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.38 Å3/Da / Density % sol: 48.44 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.38→36.72 Å / Num. obs: 29983 / % possible obs: 89.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 22.65 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 11.1
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.4 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FT4

5ft4


Resolution: 2.384→36.721 Å / SU ML: 0.27 / σ(F): 1.9 / Phase error: 21.21 / Stereochemistry target values: ML / Details: U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflection
Rfree0.2245 1490 5 %
Rwork0.1669 --
obs0.1697 29928 88.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.5 Å2
Refinement stepCycle: LAST / Resolution: 2.384→36.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6078 0 117 299 6494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046339
X-RAY DIFFRACTIONf_angle_d0.7748621
X-RAY DIFFRACTIONf_dihedral_angle_d13.8162277
X-RAY DIFFRACTIONf_chiral_restr0.052963
X-RAY DIFFRACTIONf_plane_restr0.0031123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3843-2.46130.30021430.22962626X-RAY DIFFRACTION92
2.4613-2.54920.26921420.20672610X-RAY DIFFRACTION91
2.5492-2.65130.27031260.19512599X-RAY DIFFRACTION90
2.6513-2.77190.27691430.19822598X-RAY DIFFRACTION91
2.7719-2.9180.24831250.18792592X-RAY DIFFRACTION90
2.918-3.10070.25931430.18812582X-RAY DIFFRACTION90
3.1007-3.340.22991260.17792583X-RAY DIFFRACTION89
3.34-3.67580.21221360.15312557X-RAY DIFFRACTION88
3.6758-4.2070.19611260.13322555X-RAY DIFFRACTION87
4.207-5.29790.16591430.13232548X-RAY DIFFRACTION86
5.2979-36.72510.1961370.14992588X-RAY DIFFRACTION84
Refinement TLS params.Method: refined / Origin x: 21.4065 Å / Origin y: 44.2324 Å / Origin z: 17.57 Å
111213212223313233
T0.1672 Å20.0117 Å2-0.0052 Å2-0.2175 Å2-0.0176 Å2--0.1954 Å2
L0.1573 °20.1071 °20.0108 °2-0.8888 °2-0.5273 °2--0.806 °2
S0.0008 Å °0.0252 Å °-0.0374 Å °-0.0788 Å °0.0382 Å °0.037 Å °0.0907 Å °-0.0671 Å °-0.0442 Å °
Refinement TLS groupSelection details: ALL

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