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

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Basic information

Entry
Database: PDB / ID: 7ces
TitleCrystal structure of L-cycloserine-bound form 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
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: 2.2 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)46,9573
Polymers46,5201
Non-polymers4372
Water2,972165
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9146
Polymers93,0392
Non-polymers8754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area7500 Å2
ΔGint-24 kcal/mol
Surface area28070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.700, 92.700, 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

#1: Protein Cysteine desulfurase SufS


Mass: 46519.512 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.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 64.21 %
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-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40.14 Å / Num. obs: 33104 / % possible obs: 100 % / Redundancy: 19.749 % / Biso Wilson estimate: 48.257 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.09 / Χ2: 0.944 / Net I/σ(I): 24.43 / Num. measured all: 653777 / Scaling rejects: 41
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
2.2-2.318.0260.8893.4273133405940570.8840.914100
2.3-2.520.5570.585.82129817631563150.9530.594100
2.5-2.819.9630.30810.48128863645564550.9870.316100
2.8-3.419.9760.12723.38140994705970580.9980.131100
3.4-420.260.064670708349034900.9990.062100
4-619.6620.04361.38778213958395810.044100
6-1018.990.0467.8325921136513650.9990.041100
10-40.1416.0590.04472.1965204144060.9990.04598.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZS9

5zs9


Resolution: 2.2→40.14 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 1655 5 %
Rwork0.1786 31447 -
obs0.1797 33102 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.75 Å2 / Biso mean: 50.4189 Å2 / Biso min: 25.27 Å2
Refinement stepCycle: final / Resolution: 2.2→40.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 29 165 3418
Biso mean--55.59 50.43 -
Num. residues----414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.260.27791370.224625952732
2.26-2.340.23391350.206825732708
2.34-2.420.2321370.196725892726
2.42-2.520.24811350.196825782713
2.52-2.630.23741370.184926002737
2.63-2.770.19431360.191725822718
2.77-2.950.241380.195926122750
2.95-3.170.20361370.190426152752
3.17-3.490.19461380.191426132751
3.49-40.18251380.166826332771
4-5.030.16831410.148826782819
5.04-40.140.19881460.178627792925
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)
15.78330.0291.18643.03340.78212.83140.1602-0.16350.23460.3133-0.1194-0.4855-0.54580.40410.06240.4181-0.11980.04120.317-0.06190.3898-26.588316.2916-13.6159
24.7279-1.7809-2.42564.33650.95823.693-0.0225-0.0787-0.330.2047-0.08170.2270.6150.34790.16780.34390.0079-0.0630.29340.02080.223-34.7689-8.8506-13.503
32.2493-0.20310.08482.9771-0.27471.90640.1198-0.22350.15360.431-0.15010.8046-0.1636-0.50680.1220.3723-0.02220.13850.3972-0.09380.5027-59.072411.6451-6.6695
42.42341.00820.1722.39760.70312.15010.18-0.1861-0.08060.2997-0.18380.36410.1653-0.2302-0.00950.3604-0.02840.04460.3017-0.00790.3556-51.1403-1.3994-9.8694
51.33020.43690.26653.30970.72961.2990.1171-0.23820.20040.4069-0.12230.0531-0.12250.0222-0.04250.3666-0.04670.05090.3272-0.02980.2387-39.550312.7421-6.7706
63.390.6970.17613.29560.2061.846-0.20190.32370.7731-0.42390.1380.2041-0.73180.06850.01540.6736-0.08520.01020.3846-0.03610.5124-38.587631.7937-18.0995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 34 )A-1 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 78 )A35 - 78
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 198 )A79 - 198
4X-RAY DIFFRACTION4chain 'A' and (resid 199 through 263 )A199 - 263
5X-RAY DIFFRACTION5chain 'A' and (resid 264 through 330 )A264 - 330
6X-RAY DIFFRACTION6chain 'A' and (resid 331 through 412 )A331 - 412

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