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- PDB-5ft6: Crystal structure of the cysteine desulfurase CsdA (S-sulfonic ac... -

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Basic information

Entry
Database: PDB / ID: 5ft6
TitleCrystal structure of the cysteine desulfurase CsdA (S-sulfonic acid) from Escherichia coli at 2.050 Angstroem resolution
ComponentsCYSTEINE 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 / Cysteine desulfurase CsdA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.049 Å
AuthorsFernandez, F.J. / Arda, A. / Lopez-Estepa, M. / Aranda, J. / Penya-Soler, E. / Garces, F. / Round, A. / Campos-Oliva, R. / Bruix, M. / Coll, M. ...Fernandez, F.J. / Arda, A. / Lopez-Estepa, M. / Aranda, J. / Penya-Soler, E. / Garces, 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

Downloads & links

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Assembly

Deposited unit
A: CYSTEINE DESULFURASE CSDA
B: CYSTEINE DESULFURASE CSDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,24315
Polymers86,7082
Non-polymers1,53513
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-43.8 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.966, 99.786, 105.748
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: (0.2105, 0.9635, 0.1652), (0.9649, -0.2319, 0.1229), (0.1568, 0.1335, -0.9786)
Vector: -16.0211, 24.5116, -26.115)

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Components

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


Mass: 43354.047 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
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 694 / 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: 2.32 Å3/Da / Density % sol: 47.05 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.05→39.8 Å / Num. obs: 50628 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 21.74 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.5
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.2 / % possible all: 92.5

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Processing

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

5ft4


Resolution: 2.049→39.796 Å / SU ML: 0.2 / σ(F): 1.23 / Phase error: 18.54 / Stereochemistry target values: ML / Details: U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflection
Rfree0.1907 4863 5.1 %
Rwork0.1545 --
obs0.1563 50559 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / ksol: 0.9 e/Å3
Displacement parametersBiso mean: 28.02 Å2
Refinement stepCycle: LAST / Resolution: 2.049→39.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6076 0 98 694 6868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036433
X-RAY DIFFRACTIONf_angle_d0.818773
X-RAY DIFFRACTIONf_dihedral_angle_d13.3182320
X-RAY DIFFRACTIONf_chiral_restr0.043979
X-RAY DIFFRACTIONf_plane_restr0.0031149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0492-2.07250.29221140.2572523X-RAY DIFFRACTION81
2.0725-2.09680.26031380.24142756X-RAY DIFFRACTION89
2.0968-2.12240.25521420.22362850X-RAY DIFFRACTION92
2.1224-2.14930.22561600.21612970X-RAY DIFFRACTION97
2.1493-2.17760.24191830.2153098X-RAY DIFFRACTION99
2.1776-2.20740.26441630.20323074X-RAY DIFFRACTION100
2.2074-2.23890.23531690.18523081X-RAY DIFFRACTION100
2.2389-2.27230.25371700.19263066X-RAY DIFFRACTION100
2.2723-2.30780.24671510.17993115X-RAY DIFFRACTION100
2.3078-2.34570.23631790.17993094X-RAY DIFFRACTION100
2.3457-2.38610.22021450.16543070X-RAY DIFFRACTION100
2.3861-2.42950.17851420.16473101X-RAY DIFFRACTION100
2.4295-2.47620.24471570.16883066X-RAY DIFFRACTION100
2.4762-2.52680.20021740.16393121X-RAY DIFFRACTION100
2.5268-2.58170.20841550.16563044X-RAY DIFFRACTION100
2.5817-2.64170.21261670.15663132X-RAY DIFFRACTION100
2.6417-2.70780.1911710.15683086X-RAY DIFFRACTION100
2.7078-2.7810.21881720.14933079X-RAY DIFFRACTION100
2.781-2.86280.18681520.14713080X-RAY DIFFRACTION100
2.8628-2.95520.17711870.1413052X-RAY DIFFRACTION100
2.9552-3.06070.19441810.1373063X-RAY DIFFRACTION100
3.0607-3.18320.18211480.13543126X-RAY DIFFRACTION100
3.1832-3.3280.17921810.13223074X-RAY DIFFRACTION100
3.328-3.50340.14521700.12393074X-RAY DIFFRACTION100
3.5034-3.72280.17181540.12033105X-RAY DIFFRACTION100
3.7228-4.00990.11271360.11793111X-RAY DIFFRACTION100
4.0099-4.4130.15011580.11753096X-RAY DIFFRACTION100
4.413-5.05050.14391650.12253076X-RAY DIFFRACTION100
5.0505-6.35890.20411940.16793055X-RAY DIFFRACTION100
6.3589-39.80390.19731850.19163065X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -16.1902 Å / Origin y: 6.608 Å / Origin z: -14.0918 Å
111213212223313233
T0.027 Å2-0.0188 Å20.0006 Å2--0.0118 Å2-0.0569 Å2---0.1156 Å2
L1.8381 °2-0.3035 °20.0604 °2-0.9159 °2-0.1331 °2--0.2782 °2
S-0.0008 Å °0.0641 Å °-0.2301 Å °0.0382 Å °-0.0191 Å °-0.0714 Å °0.0127 Å °0.0267 Å °0.0113 Å °
Refinement TLS groupSelection details: ALL

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