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- PDB-7e6c: Crystal structure of L-cycloserine-bound form of cysteine desulfu... -

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Basic information

Entry
Database: PDB / ID: 7e6c
TitleCrystal structure of L-cycloserine-bound form of cysteine desulfurase SufS C361A from Bacillus subtilis
ComponentsCysteine desulfurase SufS
KeywordsBIOSYNTHETIC PROTEIN / cysteine desulfurase / PLP-dependent enzyme / cysteine metabolism / cycloserine / inhibitor / Fe-S cluster biosynthesis
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-7TS / DI(HYDROXYETHYL)ETHER / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsNakamura, R. / Takahashi, Y. / Fujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K14510 Japan
CitationJournal: Febs J. / Year: 2022
Title: Cycloserine enantiomers inhibit PLP-dependent cysteine desulfurase SufS via distinct mechanisms.
Authors: Nakamura, R. / Ogawa, S. / Takahashi, Y. / Fujishiro, T.
History
DepositionFeb 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)48,32716
Polymers46,5551
Non-polymers1,77315
Water4,504250
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,65532
Polymers93,1092
Non-polymers3,54630
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area14300 Å2
ΔGint65 kcal/mol
Surface area28250 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: 46554.520 Da / Num. of mol.: 1 / Mutation: C361A
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) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: O32164, cysteine desulfurase

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Non-polymers , 5 types, 265 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-7TS / (5-hydroxy-6-methyl-4-{[(3-oxo-2,3-dihydro-1,2-oxazol-4-yl)amino]methyl}pyridin-3-yl)methyl dihydrogen phosphate


Mass: 331.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N3O7P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 64.26 %
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: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2020
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: 1.73→46.44 Å / Num. obs: 67513 / % possible obs: 100 % / Redundancy: 18.821 % / Biso Wilson estimate: 39.397 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.055 / Χ2: 1.066 / Net I/σ(I): 28.77 / Num. measured all: 1270688 / Scaling rejects: 32
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
1.73-1.8318.4510.7983.7219097310352103500.9130.82100
1.83-218.2740.377.9324123613201132010.9810.38100
2-2.320.1160.15320.3229898914863148630.9970.157100
2.3-2.619.3560.08735.03170915883088300.9990.089100
2.6-318.4620.0647.14128332695169510.9990.062100
3-418.530.04462.351402557569756910.045100
4-616.9450.03766.44673053972397210.038100
6-1019.1080.0371.22261211367136710.031100
10-46.4416.0050.02665.0365624184100.9990.02698.1

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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: 1.73→46.44 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.888 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1766 3376 5 %RANDOM
Rwork0.1524 ---
obs0.1536 64138 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.15 Å2 / Biso mean: 38.989 Å2 / Biso min: 20.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.73→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 117 250 3591
Biso mean--59.5 47.11 -
Num. residues----413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0123498
X-RAY DIFFRACTIONr_angle_refined_deg2.4621.6424727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54323.636176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12315571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6171515
X-RAY DIFFRACTIONr_chiral_restr0.2070.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022624
LS refinement shellResolution: 1.73→1.775 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 247 -
Rwork0.206 4694 -
all-4941 -
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)
10.59390.31240.29840.20730.18010.5936-0.0082-0.0904-0.0351-0.03760.0343-0.02270.12030.0934-0.02610.1330.0149-0.00670.2033-0.00840.169537.8903-52.2424-36.8842
20.37440.14270.14910.1782-0.03490.3727-0.0376-0.15640.09910.00310.00060.0472-0.03730.01850.0370.1131-0.0046-0.01340.2058-0.06790.178931.5819-32.8133-30.7477
30.65110.41-0.35783.7628-5.17367.1862-0.0990.06360.1199-0.1418-0.4712-0.37410.17540.65450.57020.03-0.04370.00330.37860.04340.269767.3988-28.2979-45.5245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 56
2X-RAY DIFFRACTION2A57 - 392
3X-RAY DIFFRACTION3A393 - 412

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