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- PDB-7e6a: Crystal structure of cysteine desulfurase SufS C361A from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 7e6a
TitleCrystal structure 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
DI(HYDROXYETHYL)ETHER / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,96813
Polymers46,7831
Non-polymers1,18512
Water3,711206
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,93626
Polymers93,5652
Non-polymers2,37124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area12440 Å2
ΔGint33 kcal/mol
Surface area28580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.600, 92.600, 129.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cysteine desulfurase SufS


Mass: 46782.637 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
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
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: 3.42 Å3/Da / Density % sol: 63.99 %
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: 1.96→46.34 Å / Num. obs: 46459 / % possible obs: 99.8 % / Redundancy: 18.653 % / Biso Wilson estimate: 43.776 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.044 / Χ2: 0.95 / Net I/σ(I): 39.84 / Num. measured all: 866617
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
1.96-2.0612.1580.3716.4676596636963000.9610.38798.9
2.06-2.219.1150.20914.34134932705970590.9930.215100
2.2-2.520.8740.11825.9621685710389103890.9980.121100
2.5-319.9840.06345.45188268942194210.9990.065100
3-418.9950.03970.741437707569756910.041100
4-619.2780.03284.24760723946394610.033100
6-1017.2140.02981.02235661369136910.03100
10-46.3416.1480.02979.94655641240610.02998.5

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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: 1.96→46.34 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.196 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1786 2323 5 %RANDOM
Rwork0.1548 ---
obs0.156 44136 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.85 Å2 / Biso mean: 43.84 Å2 / Biso min: 23.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.96→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 78 206 3513
Biso mean--69.97 48.57 -
Num. residues----412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0123410
X-RAY DIFFRACTIONr_angle_refined_deg2.3781.6354605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5535423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42723.353173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26515562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0551516
X-RAY DIFFRACTIONr_chiral_restr0.1920.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022540
LS refinement shellResolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 167 -
Rwork0.167 3182 -
all-3349 -
obs--98.27 %
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)
10.09350.1446-0.06140.970.22060.57970.1111-0.0408-0.01460.0134-0.0691-0.0289-0.06820.1927-0.0420.2035-0.06180.0120.1725-0.02490.1749-26.974411.6425-15.2891
20.14610.11770.08510.52270.29890.23970.15140.0037-0.00240.1439-0.17840.11680.0977-0.02690.0270.2268-0.02440.02660.1676-0.04270.1736-45.5676-5.7023-11.4313
30.18720.04110.17140.73310.11520.40340.0949-0.03690.03260.1524-0.14750.1626-0.0524-0.04260.05260.2095-0.03850.11040.1367-0.08370.2018-56.04411.3615-5.9431
40.5671-0.00270.73070.18550.27452.09230.10320.0409-0.04710.1554-0.07410.13130.2443-0.0456-0.02920.227-0.08590.05370.1069-0.05930.2525-56.3842-14.1889-16.8524
50.71010.65131.15310.61011.04662.13230.1234-0.0507-0.0690.1204-0.0804-0.0338-0.01080.0002-0.04290.2366-0.0436-0.00980.1582-0.01620.1723-36.9457-1.5658-11.8379
60.14370.17840.048.1061-0.27990.56720.1294-0.05220.02620.2617-0.04940.0449-0.01450.0897-0.080.2593-0.07020.01270.1406-0.05750.1011-32.789415.25810.3446
70.24550.31180.45751.99710.20940.9817-0.0654-0.02110.0772-0.1817-0.03040.1513-0.18920.04050.09580.2844-0.1340.01390.1477-0.09530.1676-36.094134.7261-6.1633
81.0020.6344-0.521.1539-0.0270.6907-0.032-0.08020.07-0.105-0.09250.1507-0.22530.09820.12450.3012-0.05710.00110.0669-0.03130.1716-39.637829.9243-15.7188
90.8619-0.0961-0.15130.36250.38390.45320.0093-0.0181-0.0243-0.0646-0.05010.0833-0.1721-0.00590.04080.2969-0.0570.04010.0772-0.07940.1835-44.535124.548-13.9303
102.1148-0.82942.31543.0781-1.53442.6775-0.30210.11050.2716-0.2008-0.002-0.1459-0.2580.11190.30410.4014-0.15710.04130.0669-0.03770.1981-32.677940.4873-20.6463
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 45
2X-RAY DIFFRACTION2A46 - 109
3X-RAY DIFFRACTION3A110 - 247
4X-RAY DIFFRACTION4A248 - 272
5X-RAY DIFFRACTION5A273 - 292
6X-RAY DIFFRACTION6A293 - 306
7X-RAY DIFFRACTION7A307 - 321
8X-RAY DIFFRACTION8A322 - 356
9X-RAY DIFFRACTION9A357 - 385
10X-RAY DIFFRACTION10A386 - 412

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