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- PDB-7xej: SufS with D-cysteine for 5 min -

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Basic information

Entry
Database: PDB / ID: 7xej
TitleSufS with D-cysteine for 5 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-9PV / 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: 1.74 Å
AuthorsNakamiura, 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
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 1.2Apr 2, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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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)47,89211
Polymers46,5871
Non-polymers1,30510
Water6,918384
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,78422
Polymers93,1732
Non-polymers2,61120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area11600 Å2
ΔGint28 kcal/mol
Surface area28720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.900, 92.900, 129.400
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 , 5 types, 394 molecules

#2: Chemical ChemComp-9PV / (2~{S})-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-sulfanyl-propanoic acid


Mass: 350.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 384 / 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: 3.46 Å3/Da / Density % sol: 64.45 %
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
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.74→46.45 Å / Num. obs: 66778 / % possible obs: 100 % / Redundancy: 10.153 % / Biso Wilson estimate: 36.921 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.068 / Χ2: 0.897 / Net I/σ(I): 19.05 / Num. measured all: 677985 / Scaling rejects: 57
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
1.74-1.8410.3930.7923.0210595210200101950.8460.833100
1.84-210.40.4095.8412821512330123280.9620.43100
2-2.29.7290.19311.3110588610885108840.9880.204100
2.2-2.510.610.11219.2811128710489104890.9960.118100
2.5-310.0870.07228.6195764949494940.9980.075100
3-49.9490.04940.6975723761176110.9990.051100
4-69.6010.04445.3638309399039900.9990.046100
6-109.710.0446.1313370137713770.9990.042100
10-46.458.4850.0443.7234794204100.9980.04297.6

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Processing

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

5zs9


Resolution: 1.74→46.45 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.888 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1756 3339 5 %RANDOM
Rwork0.1446 ---
obs0.1462 63441 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: 115.06 Å2 / Biso mean: 35.484 Å2 / Biso min: 17.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.74→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 85 384 3694
Biso mean--53.79 48.42 -
Num. residues----413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0123384
X-RAY DIFFRACTIONr_angle_refined_deg2.6291.644572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1535416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35423.609169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35815556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4491514
X-RAY DIFFRACTIONr_chiral_restr0.2260.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022528
LS refinement shellResolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 245 -
Rwork0.218 4666 -
all-4911 -
obs--99.96 %
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)
10.04330.1441-0.00980.8012-0.34020.39250.0245-0.02390.0072-0.00480.01640.03690.0196-0.1254-0.04090.0727-0.02230.00050.07340.01850.069228.0994-7.8146-15.7349
20.160.4542-0.12185.8021-1.75130.53050.11780.1318-0.02920.3771-0.1829-0.2046-0.10330.07440.06510.17380.05950.00390.1865-0.01590.037636.445120.5072-18.0835
30.09390.0563-0.10090.3403-0.13790.27670.014-0.0387-0.00930.0581-0.053-0.07060.01520.0110.0390.0795-0.0197-0.03350.04350.02890.06949.3343-10.6848-9.1264
41.7276-0.8795-1.88192.53951.5582.2227-0.22340.1415-0.1999-0.1180.02180.02990.1687-0.12330.20160.225-0.09960.00520.04730.00130.06933.3287-40.7549-21.0761
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 53
2X-RAY DIFFRACTION2A54 - 60
3X-RAY DIFFRACTION3A61 - 385
4X-RAY DIFFRACTION4A386 - 413

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