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- PDB-9jxt: An aldehyde-containing intermediate of SufS in complex with (2R,3... -

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Basic information

Entry
Database: PDB / ID: 9jxt
TitleAn aldehyde-containing intermediate of SufS in complex with (2R,3R)-3-ethoxycarbonylaziridine-2-carboxylic acid
ComponentsCysteine desulfurase SufS
KeywordsBIOSYNTHETIC PROTEIN / Cysteine desulfurase
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
: / DI(HYDROXYETHYL)ETHER / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNakamura, R. / Fujishiro, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H04542 Japan
New Energy and Industrial Technology Development Organization (NEDO)22100875-0 Japan
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Discovery of an Aziridine-Based Inhibitor That Targets Cysteine Desulfurase Type II SufS via High-Throughput X‐ray Crystallography.
Authors: Fujishiro, T. / Otsuka, H. / Nakamura, R. / Fujihara, T.
History
DepositionOct 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)47,0253
Polymers46,5871
Non-polymers4382
Water2,954164
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0506
Polymers93,1732
Non-polymers8774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area7480 Å2
ΔGint-21 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.700, 92.700, 128.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#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)
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.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-A1L40 / (2~{S})-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-oxidanylidene-propanoic acid


Mass: 332.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
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: 3.42 Å3/Da / Density % sol: 64 %
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 6M / Detector: PIXEL / Date: Nov 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 32955 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.068 / Net I/σ(I): 23.67
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.2-2.30.83240370.8280.8771
2.3-2.40.61734130.880.6511
2.4-2.50.47928840.9320.5051
2.5-2.60.32824650.9720.3461
2.6-2.70.27321130.9820.2871
2.7-2.80.21818450.9870.231
2.8-2.90.17615700.9910.1851
2.9-30.13114000.9950.1381
3-3.10.10712140.9960.1141
3.1-3.30.08120140.9980.0861
3.3-3.50.06115780.9990.0641
3.5-40.04427220.9990.0461
4-4.50.03416480.9990.0361
4.5-50.0310650.9990.0311
5-60.029122210.0311
6-100.023135710.0241
10-500.01740810.0181

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KFY

6kfy


Resolution: 2.2→46.35 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 9.028 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21223 1648 5 %RANDOM
Rwork0.1741 ---
obs0.17602 31304 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 mean: 49.817 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å2-0 Å2
2---0.09 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: 1 / Resolution: 2.2→46.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3173 0 29 164 3366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123288
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.834468
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.636514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0610548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022500
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_it3.353.5961636
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.3126.4342043
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1733.9421652
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.67545.4114342
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 120 -
Rwork0.242 2286 -
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)
10.0320.1163-0.02841.01710.25720.70720.0616-0.026-0.0090.0958-0.0907-0.0285-0.02180.14540.0290.1579-0.0451-0.00390.1208-0.01110.0469-28.46566.629-15.2125
20.1652-0.01040.04610.61540.06450.35970.1461-0.02760.00780.1925-0.1930.23610.02450.02580.04680.2004-0.09850.08910.0801-0.08080.1039-52.22824.1629-8.105
30.2105-0.0159-0.12840.94030.59550.47790.1068-0.09190.0802-0.0384-0.12030.1213-0.16580.01190.01350.2523-0.12010.07030.0895-0.06560.0536-38.337930.0058-13.2396
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 56
2X-RAY DIFFRACTION2A57 - 300
3X-RAY DIFFRACTION3A301 - 406

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