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- PDB-7e6f: Crystal structure of PMP-bound form of cysteine desulfurase SufS ... -

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Basic information

Entry
Database: PDB / ID: 7e6f
TitleCrystal structure of PMP-bound form of cysteine desulfurase SufS R376A from Bacillus subtilis in L-cycloserine-inhibition
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 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...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 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 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)46,9174
Polymers46,5001
Non-polymers4163
Water1448
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8348
Polymers93,0012
Non-polymers8336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area9210 Å2
ΔGint-16 kcal/mol
Surface area28280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.800, 92.800, 129.500
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: 46500.465 Da / Num. of mol.: 1 / Mutation: R376A
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.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.46 Å3/Da / Density % sol: 64.47 %
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: 2.74→46.44 Å / Num. obs: 17471 / % possible obs: 99.9 % / Redundancy: 20.225 % / Biso Wilson estimate: 75.225 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.113 / Χ2: 0.86 / Net I/σ(I): 19.74 / Num. measured all: 353349 / Scaling rejects: 23
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
2.74-2.8420.0680.9214.3935038174617460.9180.945100
2.84-321.5030.6326.5450662235623560.9670.647100
3-3.221.5390.3989.8149562230123010.9850.407100
3.2-3.521.1850.22215.2854107255425540.9950.227100
3.5-420.5860.12323.356386274027390.9980.126100
4-618.4730.08232.0973746399239920.9980.084100
6-1019.9180.07639.1227288137113700.9960.07899.9
10-46.4415.8840.07935.6965604204130.9970.08298.3

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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: 2.74→46.44 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 19.613 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.431 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 874 5 %RANDOM
Rwork0.1645 ---
obs0.1669 16597 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173.62 Å2 / Biso mean: 75.465 Å2 / Biso min: 39.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.33 Å2
Refinement stepCycle: final / Resolution: 2.74→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 27 8 3234
Biso mean--75.16 69.12 -
Num. residues----411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123291
X-RAY DIFFRACTIONr_angle_refined_deg2.0551.6324467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5985410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45523.742163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40115547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8291513
X-RAY DIFFRACTIONr_chiral_restr0.1370.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022479
LS refinement shellResolution: 2.74→2.811 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 64 -
Rwork0.222 1220 -
all-1284 -
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)
10.44170.0904-0.06620.3322-0.17520.41740.01-0.149-0.09210.0105-0.0193-0.0274-0.0086-0.00350.00930.02370.0006-0.00030.08760.05850.085-28.535635.3532-30.7289
24.24620.4596-2.12860.0528-0.31983.76910.0053-0.4957-0.41010.0001-0.0463-0.038-0.0030.45210.0410.00430.0148-0.00030.12310.03560.1666-3.414737.9216-40.3305
31.0410.2586-0.31620.39130.07850.3496-0.0252-0.0557-0.07250.0387-0.02860.03980.024-0.0990.05380.0236-0.01110.02410.12810.030.0672-48.134934.8548-34.5416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 247
2X-RAY DIFFRACTION2A248 - 266
3X-RAY DIFFRACTION3A267 - 411

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