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- PDB-7ceq: Crystal structure of cysteine desulfurase SufS H121A from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 7ceq
TitleCrystal structure of cysteine desulfurase SufS H121A 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: 2 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
DepositionJun 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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)46,8293
Polymers46,6161
Non-polymers2122
Water3,225179
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6576
Polymers93,2332
Non-polymers4244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area8020 Å2
ΔGint-19 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.500, 92.500, 128.600
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: 46616.430 Da / Num. of mol.: 1 / Mutation: H121A
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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.4 Å3/Da / Density % sol: 63.8 %
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: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 13, 2019
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: 2→43.52 Å / Num. obs: 43589 / % possible obs: 100 % / Redundancy: 20.14 % / Biso Wilson estimate: 41.91 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 19.52 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 3.86 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZS9

5zs9


Resolution: 2→43.52 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.185 2180 5 %
Rwork0.169 --
obs0.17 43587 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.59 Å2
Refinement stepCycle: LAST / Resolution: 2→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3239 0 14 179 3432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.24821340.21472539X-RAY DIFFRACTION100
2.04-2.090.25691350.19392570X-RAY DIFFRACTION100
2.09-2.140.22161350.17632558X-RAY DIFFRACTION100
2.14-2.20.19921340.1722558X-RAY DIFFRACTION100
2.2-2.270.24021350.17592556X-RAY DIFFRACTION100
2.27-2.340.2041330.1722535X-RAY DIFFRACTION100
2.34-2.420.19551360.17222585X-RAY DIFFRACTION100
2.42-2.520.19481350.17192557X-RAY DIFFRACTION100
2.52-2.630.19411360.17142581X-RAY DIFFRACTION100
2.63-2.770.18721350.17712564X-RAY DIFFRACTION100
2.77-2.950.21361350.1872574X-RAY DIFFRACTION100
2.95-3.170.18261370.18552608X-RAY DIFFRACTION100
3.17-3.490.2011370.18352591X-RAY DIFFRACTION100
3.49-40.16931380.15422619X-RAY DIFFRACTION100
4-5.030.14871390.1412643X-RAY DIFFRACTION100
5.04-43.520.17821460.16892769X-RAY DIFFRACTION100
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)
13.61060.2644-0.3883.61360.04291.60630.1759-0.2399-0.12950.1262-0.05770.39860.3247-0.3236-0.06280.3614-0.1041-0.03640.29490.06660.313226.5743-16.2873-13.6
21.8376-0.58930.59441.7453-0.29411.72790.0988-0.00390.14970.1588-0.138-0.3333-0.20450.080.03390.2886-0.0598-0.01180.23520.03110.261343.45794.5707-12.1679
31.35720.0265-0.00091.466-0.04431.280.0993-0.1726-0.14410.263-0.1047-0.4190.08070.25680.00830.3149-0.0454-0.09780.29890.05580.331453.556-6.0605-7.9163
41.40520.26170.03653.4186-0.78820.39510.04-0.1413-0.21150.3891-0.0864-0.18980.281-0.05310.05790.5257-0.0714-0.05490.34830.10530.352537.2112-27.3754-3.4253
53.5584-0.15461.19081.15680.72282.8308-0.13710.39740.0668-0.4674-0.0172-0.38830.37650.40850.17380.6109-0.05110.02470.31560.06350.428739.7887-29.2297-19.5584
62.47380.101-0.04621.77730.21791.2758-0.15570.1365-0.5552-0.0780.0684-0.0980.6155-0.06540.03580.6295-0.0829-0.0120.28450.06190.4737.748-33.2833-17.0416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -1 THROUGH 34 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 35 THROUGH 112 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 113 THROUGH 295 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 296 THROUGH 330 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 331 THROUGH 362 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 363 THROUGH 412 )

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