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- PDB-5j8q: Crystal Structure of the Cysteine Desulfurase SufS of Bacillus su... -

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Basic information

Entry
Database: PDB / ID: 5j8q
TitleCrystal Structure of the Cysteine Desulfurase SufS of Bacillus subtilis
ComponentsCysteine desulfurase SufS
KeywordsTRANSFERASE / Cysteine Desulfurase / Iron sulfur cluster / SUF-system
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding
Similarity search - Function
Cysteine desulfurase, SufS / 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, SufS / 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
ALANINE / PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsAltegoer, F. / Bange, G.
CitationJournal: Plos One / Year: 2016
Title: Crystal Structure of Bacillus subtilis Cysteine Desulfurase SufS and Its Dynamic Interaction with Frataxin and Scaffold Protein SufU.
Authors: Blauenburg, B. / Mielcarek, A. / Altegoer, F. / Fage, C.D. / Linne, U. / Bange, G. / Marahiel, M.A.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 15, 2020Group: Atomic model / Category: atom_site / Item: _atom_site.occupancy
Revision 2.1Jan 10, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3163
Polymers45,9801
Non-polymers3362
Water5,278293
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6326
Polymers91,9602
Non-polymers6724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area8060 Å2
ΔGint-32 kcal/mol
Surface area28860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.191, 93.191, 130.543
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-681-

HOH

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Components

#1: Protein Cysteine desulfurase SufS


Mass: 45979.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: sufS, csd, yurW, BSU32690 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O32164, cysteine desulfurase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 3.56 Å3/Da / Density % sol: 65.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 50 % (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.702→46.6 Å / Num. obs: 72121 / % possible obs: 97 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.07071 / Net I/σ(I): 2.7
Reflection shellResolution: 1.702→1.762 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0135refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W91

4w91


Resolution: 1.702→46.6 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.319 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14789 3577 5 %RANDOM
Rwork0.11612 ---
obs0.11771 68544 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.428 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å2-0 Å2
2--0.04 Å20 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.702→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 21 293 3538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193344
X-RAY DIFFRACTIONr_bond_other_d0.0020.023165
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9454545
X-RAY DIFFRACTIONr_angle_other_deg1.00937281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.655420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46124.545154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66415556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9341515
X-RAY DIFFRACTIONr_chiral_restr0.110.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023802
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02763
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_it2.0562.5371665
X-RAY DIFFRACTIONr_mcbond_other2.042.5351664
X-RAY DIFFRACTIONr_mcangle_it2.3853.8072081
X-RAY DIFFRACTIONr_mcangle_other2.3883.8092082
X-RAY DIFFRACTIONr_scbond_it3.2893.1021678
X-RAY DIFFRACTIONr_scbond_other3.2883.1011678
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9544.4642462
X-RAY DIFFRACTIONr_long_range_B_refined4.49822.4723932
X-RAY DIFFRACTIONr_long_range_B_other3.87421.7753803
X-RAY DIFFRACTIONr_rigid_bond_restr3.45636508
X-RAY DIFFRACTIONr_sphericity_free34.7955117
X-RAY DIFFRACTIONr_sphericity_bonded12.30256610
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 254 -
Rwork0.175 4770 -
obs--95.48 %

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