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- PDB-7xek: SufS with D-cysteine for 30 min -

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Basic information

Entry
Database: PDB / ID: 7xek
TitleSufS with D-cysteine for 30 min
ComponentsCysteine desulfurase SufS
KeywordsBIOSYNTHETIC PROTEIN / Cysteine desulfurase / Inhibitor
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
Chem-9YX / 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: 1.88 Å
AuthorsNakamura, R. / Fujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K19340 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
DepositionMar 31, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 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 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / struct
Item: _pdbx_entry_details.has_protein_modification / _struct.title
Revision 1.3Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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

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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)48,46716
Polymers46,5871
Non-polymers1,88015
Water5,188288
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,93332
Polymers93,1732
Non-polymers3,76030
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area13200 Å2
ΔGint51 kcal/mol
Surface area29720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.800, 92.800, 128.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cysteine desulfurase SufS


Mass: 46586.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 6 types, 303 molecules

#2: Chemical ChemComp-9YX / (2~{S},4~{S})-2-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-1,3-thiazolidine-4-carboxylic acid


Mass: 350.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.44 Å3/Da / Density % sol: 64.24 %
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-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 26, 2019
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→46.4 Å / Num. obs: 52726 / % possible obs: 99.8 % / Redundancy: 6.556 % / Biso Wilson estimate: 37.116 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.056 / Χ2: 0.918 / Net I/σ(I): 21.75 / Num. measured all: 345688 / Scaling rejects: 108
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
1.88-1.986.7770.6632.7251127754775440.8240.717100
1.98-2.26.4820.3045.817851712116121130.960.33100
2.2-2.56.8160.14712.377075410387103800.9890.15999.9
2.5-36.4470.07124.1160768945094260.9970.07799.7
3-46.4280.03545.448445756975370.9990.03899.6
4-66.4060.02261.5725356397239580.9990.02499.6
6-106.0460.01763.2482351367136210.01899.6
10-46.46.1230.01369.5248641840610.01497.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZS9

5zs9


Resolution: 1.88→46.4 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.077 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1794 2637 5 %RANDOM
Rwork0.1489 ---
obs0.1504 50090 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.14 Å2 / Biso mean: 36.538 Å2 / Biso min: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 1.88→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 123 288 3636
Biso mean--58.99 45.06 -
Num. residues----413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0123404
X-RAY DIFFRACTIONr_angle_refined_deg2.451.6434581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5485412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07323.533167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63515552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6371514
X-RAY DIFFRACTIONr_chiral_restr0.1930.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022508
LS refinement shellResolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 195 -
Rwork0.251 3699 -
all-3894 -
obs--99.95 %
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)
13.47892.89411.53324.0620.15781.44380.21470.0768-0.47760.27980.2258-0.0990.0568-0.0308-0.44050.07620.1108-0.06550.1993-0.06590.170947.4954-53.8441-27.2567
20.51450.27250.19180.15370.09980.47060.0298-0.04380.01650.00480.01230.00780.13320.0781-0.0420.10390.0077-0.01750.1548-0.01160.116935.8962-52.0621-39.0309
30.27580.16660.10450.2455-0.00580.2991-0.0222-0.14370.0883-0.01820.00760.0486-0.003-0.03320.01460.08430.00140.00010.1574-0.06540.12723.163-32.5171-30.0125
43.43161.79550.53012.21960.36690.23290.0347-0.28070.01380.04260.0182-0.05920.12750.0085-0.05280.1101-0.0027-0.04670.2154-0.02330.036841.4013-45.167-20.8312
50.751-0.06290.21050.34510.17510.2283-0.06550.03770.1560.0040.015-0.0245-0.03210.12390.05050.0655-0.0428-0.02980.2087-0.00880.115651.1798-29.3612-34.8566
60.66950.13310.21940.5544-0.23010.21840.04670.15740.03410.0361-0.0629-0.04650.00960.11650.01620.02070.0089-0.03780.3031-0.03780.106561.2064-34.0494-39.7334
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 8
2X-RAY DIFFRACTION2A9 - 56
3X-RAY DIFFRACTION3A57 - 291
4X-RAY DIFFRACTION4A292 - 304
5X-RAY DIFFRACTION5A305 - 378
6X-RAY DIFFRACTION6A379 - 413

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