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- PDB-4lw2: Structural changes during cysteine desulfurase CsdA and sulfur-ac... -

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Basic information

Entry
Database: PDB / ID: 4lw2
TitleStructural changes during cysteine desulfurase CsdA and sulfur-acceptor CsdE interactions provide insight into the trans-persulfuration
ComponentsCysteine sulfinate desulfinase
KeywordsLYASE / cysteine desulfurase / CsdA / SufS
Function / homology
Function and homology information


sulfur compound transport / selenocysteine catabolic process / sulfur amino acid metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / L-cysteine desulfurase complex / sulfurtransferase activity / L-cysteine catabolic process ...sulfur compound transport / selenocysteine catabolic process / sulfur amino acid metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / L-cysteine desulfurase complex / sulfurtransferase activity / 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
PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase CsdA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, S. / Park, S.Y.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural changes during cysteine desulfurase CsdA and sulfur acceptor CsdE interactions provide insight into the trans-persulfuration.
Authors: Kim, S. / Park, S.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _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
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine sulfinate desulfinase
B: Cysteine sulfinate desulfinase
C: Cysteine sulfinate desulfinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6869
Polymers130,6693
Non-polymers1,0186
Water19,9431107
1
A: Cysteine sulfinate desulfinase
hetero molecules

A: Cysteine sulfinate desulfinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7916
Polymers87,1132
Non-polymers6784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7840 Å2
ΔGint-40 kcal/mol
Surface area27410 Å2
MethodPISA
2
B: Cysteine sulfinate desulfinase
C: Cysteine sulfinate desulfinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7916
Polymers87,1132
Non-polymers6784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-40 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.298, 91.441, 83.894
Angle α, β, γ (deg.)90.00, 97.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-727-

HOH

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Components

#1: Protein Cysteine sulfinate desulfinase / CSD


Mass: 43556.250 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2810, csdA, JW2781, ygdJ / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q46925, Lyases; Carbon-sulfur lyases
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1107 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 20-30% (w/v) PEG 8000, 0.05M potassium di-hydrogen phosphate, 0.1M MES, 0.1M Tris, pH 5.5-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→83.47 Å / Num. obs: 116275 / % possible obs: 100 %
Reflection shellResolution: 1.8→1.86 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C0N

1c0n


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.498 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21235 5819 5 %RANDOM
Rwork0.16473 ---
obs0.16713 110343 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å21.11 Å2
2---0.19 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9079 0 63 1107 10249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0229399
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1081.95812818
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53151209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20324.12415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82151450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3921559
X-RAY DIFFRACTIONr_chiral_restr0.1720.21450
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217225
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3191.55974
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.17929550
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.78533425
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.9074.53260
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.798→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 417 -
Rwork0.231 8021 -
obs--98.64 %

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