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- PDB-9jx7: SufS in complex with (2R,3R)-3-ethoxycarbonylaziridine-2-carboxyl... -

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Basic information

Entry
Database: PDB / ID: 9jx7
TitleSufS 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: 1.8 Å
AuthorsFujishiro, T. / Nakamura, R.
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

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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)47,3596
Polymers46,5871
Non-polymers7735
Water5,621312
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,71912
Polymers93,1732
Non-polymers1,54510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area9120 Å2
ΔGint-6 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.970, 92.970, 129.900
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.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-A1L4Z / 2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]propanedioic acid


Mass: 348.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 3.48 Å3/Da / Density % sol: 64.64 %
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: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 60716 / % possible obs: 99.5 % / Redundancy: 18.1 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.064 / Net I/σ(I): 24.79
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.90.8787640.7820.9211
1.9-2.20.368183770.9810.3791
2.2-2.30.21441530.9930.2191
2.3-2.40.17734610.9940.1811
2.4-2.50.15329380.9960.1571
2.5-2.60.12425070.9970.1271
2.6-2.70.11321630.9980.1161
2.7-30.08748980.9990.0891
3-3.50.05648760.9990.0581
3.5-40.041277210.0421
4-4.50.036168710.0371
4.5-50.034108710.0341
5-60.036123810.0371
6-100.031138010.0311
10-500.02641510.0271

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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: 1.8→46.49 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.757 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1856 3027 5 %RANDOM
Rwork0.15944 ---
obs0.16072 57496 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.921 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.8→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 51 312 3525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123284
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163084
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.8294451
X-RAY DIFFRACTIONr_angle_other_deg0.71.7597108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3555407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.024514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49310544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023812
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02708
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_it2.4842.4451628
X-RAY DIFFRACTIONr_mcbond_other2.4772.4441627
X-RAY DIFFRACTIONr_mcangle_it3.1824.3752032
X-RAY DIFFRACTIONr_mcangle_other3.1854.3762033
X-RAY DIFFRACTIONr_scbond_it4.0492.9221656
X-RAY DIFFRACTIONr_scbond_other4.0512.9191652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.795.1322416
X-RAY DIFFRACTIONr_long_range_B_refined7.52631.714370
X-RAY DIFFRACTIONr_long_range_B_other7.4431.114077
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 215 -
Rwork0.305 4071 -
obs--97.03 %
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)
10.78650.34270.16840.20290.13460.4992-0.0076-0.1146-0.011-0.03660.0353-0.0040.11440.0881-0.02760.097-0.004-0.01240.1784-0.01530.114837.9019-52.18-36.7747
20.39220.18920.07710.2363-0.0290.341-0.0132-0.21790.1667-0.0472-0.01310.09480.0131-0.03620.02630.0336-0.0043-0.01040.1962-0.11350.170523.6763-33.0683-29.9316
30.80670.18580.44440.36140.27960.4491-0.0834-0.06220.121-0.03960.0917-0.0209-0.06930.1752-0.00820.0251-0.0329-0.01490.2628-0.08790.110952.778-32.2954-34.3144
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 56
2X-RAY DIFFRACTION2A57 - 300
3X-RAY DIFFRACTION3A301 - 405

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