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- PDB-7cer: Crystal structure of D-cycloserine-bound form of cysteine desulfu... -

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Basic information

Entry
Database: PDB / ID: 7cer
TitleCrystal structure of D-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-DCS / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)47,1094
Polymers46,5201
Non-polymers5903
Water2,468137
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2188
Polymers93,0392
Non-polymers1,1796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area9710 Å2
ΔGint-15 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.500, 92.500, 128.200
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-DCS / D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE / D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE


Mass: 333.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N3O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.4 Å3/Da / Density % sol: 63.86 %
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: 2.3→43.51 Å / Num. obs: 28762 / % possible obs: 100 % / Redundancy: 9.794 % / Biso Wilson estimate: 49.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.072 / Χ2: 0.908 / Net I/σ(I): 24.65 / Num. measured all: 281700 / Scaling rejects: 27
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
2.3-2.410.3370.6553.8135043339033900.8880.69100
2.4-2.610.1620.4325.7754031531753170.9540.455100
2.6-39.3270.21110.9564307689768950.9890.223100
3-410.1180.06932.3475691748174810.9990.072100
4-68.9360.03456.6735075392539250.9990.036100
6-1010.220.02370.07137771348134810.024100
10-43.519.30.01676.87377641240610.01798.5

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Processing

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

5zs9


Resolution: 2.3→43.51 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 1439 5 %
Rwork0.1763 27323 -
obs0.1783 28762 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.36 Å2 / Biso mean: 53.5837 Å2 / Biso min: 23.82 Å2
Refinement stepCycle: final / Resolution: 2.3→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 39 137 3400
Biso mean--69.51 47.61 -
Num. residues----414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.380.2641420.218726952837
2.38-2.480.26021420.204726852827
2.48-2.590.24751420.190527012843
2.59-2.730.25751420.197827032845
2.73-2.90.27171420.203326922834
2.9-3.120.28071420.192427032845
3.12-3.440.27041440.190527442888
3.44-3.930.22881440.170327292873
3.93-4.950.16621460.148927792925
4.96-43.510.16531530.166828923045
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)
15.3377-0.1530.67037.9251.32112.94310.1284-0.31440.4010.329-0.0551-0.7756-0.5290.4685-0.08010.3765-0.13660.01870.3328-0.06260.3406-26.20716.0246-13.4967
22.7648-1.72250.10126.76192.10855.10410.2541-0.0778-0.36050.3905-0.1323-0.24410.67720.0801-0.08570.39260.0468-0.04770.39280.00620.2371-31.1906-8.2944-17.4559
32.6708-1.2351-0.22263.28820.09351.92180.1381-0.34030.15510.4448-0.14260.6312-0.2224-0.36420.00970.401-0.06990.14320.3666-0.08660.4173-54.4278.4603-6.245
41.64441.05030.7943.81611.34672.8350.1401-0.0549-0.24110.2676-0.15190.48610.3079-0.3598-0.00280.3297-0.05690.02180.3109-0.0210.3838-53.1796-6.3835-13.9272
51.3471.52750.70167.23381.56631.64820.2008-0.31150.31020.6943-0.30110.3221-0.06480.00610.09960.3741-0.05210.09230.3565-0.05990.2274-39.388312.8239-6.7356
67.2583-0.4755-4.28722.6644-3.13277.1319-0.33230.60880.056-0.51640.19780.2807-0.3049-0.49360.15420.6925-0.0997-0.03630.3577-0.07170.4677-39.648729.2953-19.7333
74.9766-0.07090.27473.0690.03691.8889-0.2930.45721.0869-0.21010.11270.0211-0.87170.1320.12650.7779-0.1198-0.00650.4178-0.05740.6037-37.520233.331-17.2838
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 57 )A35 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 221 )A58 - 221
4X-RAY DIFFRACTION4chain 'A' and (resid 222 through 263 )A222 - 263
5X-RAY DIFFRACTION5chain 'A' and (resid 264 through 330 )A264 - 330
6X-RAY DIFFRACTION6chain 'A' and (resid 331 through 362 )A331 - 362
7X-RAY DIFFRACTION7chain 'A' and (resid 363 through 412 )A363 - 412

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