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- PDB-7xeq: NifS with D-cysteine -

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Basic information

Entry
Database: PDB / ID: 7xeq
TitleNifS with D-cysteine
ComponentsCysteine desulfurase IscS
KeywordsBIOSYNTHETIC PROTEIN / Cysteine desulfurase / Inhibitor
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-9YX / ISOPROPYL ALCOHOL / Cysteine desulfurase IscS
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNakamura, R. / Fujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K14510 Japan
CitationJournal: to be published
Title: X-ray crystallographic snapshots of the thioazolidine formation upon the PLP during inhibition of SufS by D-cysteine
Authors: Nakamura, R. / Takahashi, Y. / Fujishiro, T.
History
DepositionMar 31, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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 IscS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5714
Polymers44,1251
Non-polymers4463
Water97354
1
A: Cysteine desulfurase IscS
hetero molecules

A: Cysteine desulfurase IscS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1428
Polymers88,2502
Non-polymers8926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6310 Å2
ΔGint-48 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.500, 103.500, 132.600
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 (bacteria) / Strain: ATCC 700392 / 26695 / Gene: iscS, HP_0220 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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-9YX / (2~{S},4~{S})-2-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-1,3-thiazolidine-4-carboxylic acid


Mass: 350.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 4.02 Å3/Da / Density % sol: 69.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 85 mM HEPES-NaOH, 17% (w/v) PEG4000, 15% (v/v) glycerol, 8.5% (v/v) isopropanol

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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 S 2M / Detector: PIXEL / Date: Feb 28, 2021
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: 2.9→49.14 Å / Num. obs: 16554 / % possible obs: 99.9 % / Redundancy: 12.51 % / Biso Wilson estimate: 78.961 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.078 / Χ2: 0.928 / Net I/σ(I): 23.63 / Num. measured all: 207089 / Scaling rejects: 159
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
2.9-312.7210.7913.4419857156115610.9250.825100
3-3.513.020.3477.7670568542354200.9870.36299.9
3.5-412.7220.13219.6539159308430780.9970.13899.8
4-612.1180.05937.6654228447544750.9990.062100
6-1011.4640.03453.71176781542154210.036100
10-49.1411.7130.02366.92559948347810.02499

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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: 5WT2

5wt2


Resolution: 2.9→49.14 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 28.294 / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.427 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 828 5 %RANDOM
Rwork0.181 ---
obs0.1832 15725 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 225.2 Å2 / Biso mean: 102.949 Å2 / Biso min: 43.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2---0.83 Å2-0 Å2
3---1.66 Å2
Refinement stepCycle: final / Resolution: 2.9→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 27 54 2826
Biso mean--91.49 73.14 -
Num. residues----355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122821
X-RAY DIFFRACTIONr_angle_refined_deg2.2541.6443823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9965353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14422.518139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.52415487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3041517
X-RAY DIFFRACTIONr_chiral_restr0.1620.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022095
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 59 -
Rwork0.337 1124 -
all-1183 -
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)
10.88770.53110.33051.2592-0.48922.9723-0.02670.557-0.45680.41960.05970.07420.28630.225-0.0330.4282-0.08170.16660.5195-0.27660.6803-22.8617-35.0771-3.3804
20.9204-0.2097-0.02631.4945-0.021.4653-0.07160.8401-0.14980.6085-0.1378-0.0419-0.14840.59960.20940.2613-0.1262-0.0391.08020.07870.4612-10.6515-20.1029-12.9918
32.3434-0.09071.00071.14450.54833.5964-0.0480.96090.0525-0.115-0.15960.2083-0.04650.15150.20760.1257-0.058-0.09470.9942-0.00270.1646-33.3069-22.446-29.6792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 66
2X-RAY DIFFRACTION2A67 - 261
3X-RAY DIFFRACTION3A262 - 379

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