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- PDB-7e6e: Crystal structure of PMP-bound form of cysteine desulfurase SufS ... -

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Basic information

Entry
Database: PDB / ID: 7e6e
TitleCrystal structure of PMP-bound form of cysteine desulfurase SufS R376A from Bacillus subtilis in D-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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
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: 2.28 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)47,74013
Polymers46,5001
Non-polymers1,23912
Water1,71195
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,48026
Polymers93,0012
Non-polymers2,47924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area11350 Å2
ΔGint4 kcal/mol
Surface area29880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.400, 92.400, 128.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 107 molecules

#2: 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
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.41 Å3/Da / Density % sol: 63.94 %
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
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: 2.28→46.24 Å / Num. obs: 29583 / % possible obs: 100 % / Redundancy: 19.721 % / Biso Wilson estimate: 58.813 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.068 / Χ2: 0.881 / Net I/σ(I): 29.97 / Num. measured all: 583407 / Scaling rejects: 16
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
2.28-2.3820.0920.9163.6871106353935390.9010.94100
2.38-2.720.1620.4966.86162704807080700.9740.508100
2.7-3.120.090.19416.55120600600360030.9960.199100
3.1-419.5310.06642.98122751628562850.9990.068100
4-618.8030.03874.59738973930393010.039100
6-1018.6980.02686.73252421350135010.027100
10-46.2417.5050.02194.73710741240610.02298.5

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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: 2.28→46.24 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.969 / SU B: 8.653 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1782 1479 5 %RANDOM
Rwork0.162 ---
obs0.1628 28103 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.18 Å2 / Biso mean: 58.486 Å2 / Biso min: 33.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å20 Å2
3----0.49 Å2
Refinement stepCycle: final / Resolution: 2.28→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 81 95 3385
Biso mean--74.21 54.83 -
Num. residues----412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123356
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.6354531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7455413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56123.554166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89415551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7571514
X-RAY DIFFRACTIONr_chiral_restr0.1310.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022498
LS refinement shellResolution: 2.28→2.339 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 107 -
Rwork0.22 2053 -
all-2160 -
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)
10.84970.01280.08620.12450.23560.45550.0254-0.0634-0.0740.02020.0735-0.05120.06450.1352-0.09890.12930.0429-0.03160.206-0.01790.232944.304-50.649-35.759
20.39420.15630.18270.50350.23550.26710.02-0.1270.077-0.0520.00140.09190.0633-0.0629-0.02130.132-0.00460.00880.1918-0.02630.200318.904-44.079-33.178
30.71430.07870.11230.2917-0.05530.39710.0204-0.18480.12560.0266-0.01840.0525-0.0501-0.0279-0.0020.13870.01410.00830.1766-0.07690.214724.471-29.924-29.539
48.05044.3063-0.47534.45480.04660.09550.1622-0.31970.12990.2518-0.0771-0.10090.06290.0304-0.08510.18520.0176-0.07440.286-0.04520.134542.894-44.372-20.955
51.79530.08341.09050.00430.04990.6818-0.0543-0.0220.17070.0047-0.01970.002-0.02410.05710.0740.1318-0.0171-0.05760.2582-0.05020.21253.97-30.623-27.366
60.5108-0.4670.46933.23420.70790.8918-0.05990.27010.0306-0.04370.01170.0059-0.10360.3520.04830.1116-0.0621-0.01810.2901-0.01020.208254.449-31.998-42.555
70.24130.2190.26950.32620.34670.66810.0297-0.0130.06480.0649-0.0291-0.028-0.04810.2392-0.00070.108-0.0657-0.04230.2853-0.02390.217852.544-31.846-36.882
85.475111.875-3.456331.3267-21.180335.8004-0.1081-0.3781-0.89330.1335-0.324-1.8986-0.8333-0.99290.43210.03750.0790.05820.28090.13520.32271.003-23-51.76
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 43
2X-RAY DIFFRACTION2A44 - 109
3X-RAY DIFFRACTION3A110 - 292
4X-RAY DIFFRACTION4A293 - 305
5X-RAY DIFFRACTION5A306 - 333
6X-RAY DIFFRACTION6A334 - 356
7X-RAY DIFFRACTION7A357 - 405
8X-RAY DIFFRACTION8A406 - 411

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