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- PDB-7yb3: SufS with D-cysteine for 1 min -

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Basic information

Entry
Database: PDB / ID: 7yb3
TitleSufS with D-cysteine for 1 min
ComponentsCysteine desulfurase SufS
KeywordsBIOSYNTHETIC PROTEIN / Cysteine desulfurase / iron-sulfur cluster biosynthesis / PLP-dependent enzyme
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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
D-CYSTEINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNakamura, R. / Fujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K14510 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Visualizing thiazolidine ring formation in the reaction of D-cysteine and pyridoxal-5'-phosphate within L-cysteine desulfurase SufS.
Authors: Nakamura, R. / Fujishiro, T.
History
DepositionJun 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Apr 9, 2025Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / entity_poly / entity_poly_seq / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_comp_id / _pdbx_struct_mod_residue.label_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6618
Polymers46,8151
Non-polymers8467
Water5,278293
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,32116
Polymers93,6292
Non-polymers1,69214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area10410 Å2
ΔGint12 kcal/mol
Surface area27040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.900, 92.900, 129.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cysteine desulfurase SufS


Mass: 46814.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residue 224 is used for a Lys-PLP-D-cysteine adduct as an reaction intermediate.
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: sufS, csd, yurW, BSU32690 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O32164, cysteine desulfurase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-DCY / D-CYSTEINE


Type: D-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.43 Å3/Da / Density % sol: 64.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Tris-HCl, 50 mM lithium sulfate, 50% (v/v) PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→46.49 Å / Num. obs: 60256 / % possible obs: 100 % / Redundancy: 10.182 % / Biso Wilson estimate: 40.896 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.112 / Χ2: 0.874 / Net I/σ(I): 12.33 / Num. measured all: 613504 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.910.4940.9412.4393671892789260.8020.989100
1.9-210.3360.5673.9874336719271920.9160.597100
2-2.29.7360.2897.110553410841108400.9730.306100
2.2-2.510.6180.16712.3111098010452104520.990.175100
2.5-310.1560.11417.6796378949194900.9940.121100
3-410.1020.09323.2276714759475940.9950.098100
4-69.7620.08824.8138891398439840.9940.093100
6-109.850.08825.0213475136913680.9950.09399.9
10-46.498.5980.09123.4335254184100.9930.09798.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZS9

5zs9


Resolution: 1.8→46.49 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.777 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1714 3013 5 %RANDOM
Rwork0.156 ---
obs0.1568 57244 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.94 Å2 / Biso mean: 39.539 Å2 / Biso min: 23.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2---0.05 Å20 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 1.8→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 48 293 3515
Biso mean--66.33 48.2 -
Num. residues----405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0123280
X-RAY DIFFRACTIONr_angle_refined_deg2.3541.6434433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3185402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5723.54161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26915538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4441514
X-RAY DIFFRACTIONr_chiral_restr0.1820.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022449
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 221 -
Rwork0.24 4202 -
all-4423 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.12010.32490.06771.4820.48210.96350.056-0.0492-0.0008-0.02190.0502-0.1607-0.12460.246-0.10620.0897-0.08310.02980.1276-0.04980.1033-26.68912.936-14.795
20.2170.01190.07810.60450.5220.57550.14530.0324-0.03380.1204-0.14180.10.1341-0.0395-0.00350.1253-0.01060.01220.1081-0.04730.1201-45.064-5.895-11.9
30.30480.22960.10061.27880.32040.30340.0862-0.03450.08990.2272-0.17490.2771-0.0755-0.02410.08870.1708-0.04310.09260.08-0.07390.1542-57.33813.623-5.061
42.39911.7373-2.51131.9134-2.72413.880.0506-0.2390.0734-0.00160.00780.03940.00070.003-0.05840.1303-0.00290.0390.1104-0.08090.1618-44.84413.034-14.598
50.36360.21680.08790.58260.2460.38080.0729-0.0073-0.03050.167-0.0650.08550.0830.0149-0.00790.1123-0.0420.02810.0566-0.02460.0955-48.07-5.113-11.735
61.26090.3306-0.10841.11660.71070.5855-0.0167-0.03530.1297-0.1822-0.02730.1404-0.22760.01050.0440.2562-0.0350.01440.0275-0.04880.1013-41.31628.973-12.451
70.9744-0.12790.50524.3688-1.30471.5118-0.1407-0.05490.1117-0.03180.164-0.1332-0.31720.1726-0.02330.2251-0.10790.0420.094-0.06610.1077-31.14831.524-14.31
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 43
2X-RAY DIFFRACTION2A44 - 109
3X-RAY DIFFRACTION3A110 - 223
4X-RAY DIFFRACTION4A224
5X-RAY DIFFRACTION5A225 - 300
6X-RAY DIFFRACTION6A301 - 378
7X-RAY DIFFRACTION7A379 - 405

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