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

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Basic information

Entry
Database: PDB / ID: 7cet
TitleCrystal structure of D-cycloserine-bound form of cysteine desulfurase NifS from Helicobacter pylori
ComponentsCysteine desulfurase IscS
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 / [2Fe-2S] cluster assembly / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / metal ion binding / cytoplasm
Similarity search - Function
Cysteine desulfurase NifS, proteobacteria / Cysteine desulfurase IscS / Cysteine desulfurase / 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 / ISOPROPYL ALCOHOL / Cysteine desulfurase IscS
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 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 IscS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5524
Polymers44,1251
Non-polymers4273
Water46826
1
A: Cysteine desulfurase IscS
hetero molecules

A: Cysteine desulfurase IscS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1048
Polymers88,2502
Non-polymers8546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6190 Å2
ΔGint-47 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.200, 103.200, 133.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cysteine desulfurase IscS


Mass: 44125.230 Da / Num. of mol.: 1 / Mutation: L2V, K138R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Gene: iscS, HP_0220 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: O25008, cysteine desulfurase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 4.03 Å3/Da / Density % sol: 69.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.085 M Sodium HEPES, 17% (w/v) PEG 4000, 8.5% (v/v) Isopropyl alcohol, 15% (v/v) Glycerol

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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: Jun 29, 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: 2.64→48.14 Å / Num. obs: 21427 / % possible obs: 97.97 % / Redundancy: 3.966 % / Biso Wilson estimate: 66.93 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05187 / Rpim(I) all: 0.0202 / Rrim(I) all: 0.05594 / Χ2: 1.148 / Net I/σ(I): 25.38 / Num. measured all: 156707 / Scaling rejects: 171
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2CC starRpim(I) allRrim(I) all% possible all
2.64-2.7343.9190.73122.9715963425220800.8210.950.2870.788897.6
2.74-2.94.0430.323.822771566556320.9270.36799.4
2.9-3.23.9020.176.929911783076650.9750.19697.9
3.2-43.9640.06518.224284211096108070.9970.07497.4
4-63.990.0336.5231962822180110.9990.03497.4
6-103.990.02147.6410429269526140.9990.02497
10-48.144.0070.01658.9282975770610.01893.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WT2

5wt2


Resolution: 2.64→48.14 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.917 / SU B: 20.765 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 1072 5 %RANDOM
Rwork0.1944 ---
obs0.1967 20353 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 192.45 Å2 / Biso mean: 78.403 Å2 / Biso min: 40.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.24 Å2
Refinement stepCycle: final / Resolution: 2.64→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 27 26 2834
Biso mean--77.33 57.23 -
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122877
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.6343900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2785361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33922.5144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.72115500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2241518
X-RAY DIFFRACTIONr_chiral_restr0.1460.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022165
LS refinement shellResolution: 2.64→2.708 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 77 -
Rwork0.441 1456 -
all-1533 -
obs--97.71 %
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)
11.27970.01130.85770.765-0.21132.1572-0.1150.4904-0.43170.3958-0.02160.01870.1833-0.00670.13660.3464-0.09070.1630.3368-0.20630.3795-24.6055-34.7136-2.6939
20.6077-0.2149-0.28161.45810.13490.7498-0.00190.4332-0.00760.1537-0.028-0.1618-0.0840.2480.02990.088-0.07190.02340.660.03190.2355-8.7149-18.6628-13.161
31.4861-0.45250.04721.03650.09061.4745-0.05710.8107-0.16210.034-0.14890.048-0.0394-0.04330.2060.0571-0.041-0.00430.7696-0.17330.0889-31.995-23.9693-27.4063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 59
2X-RAY DIFFRACTION2A60 - 243
3X-RAY DIFFRACTION3A244 - 385

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