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- PDB-5wt6: Cysteine persulfide intermediate of NifS from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 5wt6
TitleCysteine persulfide intermediate of NifS from Helicobacter pylori
ComponentsCysteine desulfurase IscS
KeywordsTRANSFERASE / Iron-sulfur cluster biogenesis / cysteine desulfurase
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 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Cysteine desulfurase NifS, proteobacteria / Cysteine desulfurase IscS / Cysteine desulfurase / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Chem-PDA / Cysteine desulfurase IscS
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsFujishiro, T. / Nakamura, R. / Takahashi, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS15H04472 Japan
JSPS15H06085 Japan
the Sumitomo Foundation163037 Japan
CitationJournal: To be published
Title: Structural snapshot of cysteine desulfurase NifS with L-cysteine in initiation of catalysis
Authors: Fujishiro, T. / Nakamura, R. / Takahashi, Y.
History
DepositionDec 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)44,5734
Polymers44,1571
Non-polymers4163
Water23413
1
A: Cysteine desulfurase IscS
hetero molecules

A: Cysteine desulfurase IscS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1468
Polymers88,3152
Non-polymers8326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6400 Å2
ΔGint-48 kcal/mol
Surface area26430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.750, 102.750, 131.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cysteine desulfurase IscS / Cysteine desulfurase NifS


Mass: 44157.297 Da / Num. of mol.: 1 / Mutation: L2V, K138R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: iscS, HP_0220 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / 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 / Comment: alkaloid*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PDA / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID / PYRIDOXYL-ALANINE-5-PHOSPHATE


Mass: 320.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N2O7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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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: 3.94 Å3/Da / Density % sol: 68.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HEPES/NaOH, PEG 4000, glycerol, isopropanol, L-cysteine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 20, 2016
RadiationMonochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 11147 / % possible obs: 100 % / Redundancy: 14 % / Net I/σ(I): 13.03
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 2.37 / Num. measured obs: 15694 / Num. unique all: 1081 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ECX

1ecx


Resolution: 3.3→48.847 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.53
RfactorNum. reflection% reflection
Rfree0.2448 558 5.01 %
Rwork0.2167 --
obs0.2181 11146 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→48.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2825 0 26 13 2864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032900
X-RAY DIFFRACTIONf_angle_d0.6733928
X-RAY DIFFRACTIONf_dihedral_angle_d11.9331735
X-RAY DIFFRACTIONf_chiral_restr0.048453
X-RAY DIFFRACTIONf_plane_restr0.004504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3.3-3.6320.3351360.276125761081
3.632-4.15730.2691360.22642593
4.1573-5.23690.22041390.20432640
5.2369-48.85210.21731470.20062779
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)
13.5401-0.51561.91153.2869-0.84656.16160.14120.2786-0.7996-0.0927-0.09540.10761.03810.0292-0.09940.49680.03130.03720.3862-0.05540.5995-24.4131-34.6551-2.4789
26.24780.6854-1.64416.0226-0.72946.2846-0.01720.65590.45920.578-0.1496-1.2418-0.05161.21360.09590.3228-0.0359-0.09060.80410.13770.6618-8.4796-21.4157-5.7617
35.27380.3211-0.66594.20950.24424.1527-0.39851.25360.8419-0.97920.1346-0.8677-0.09621.37010.22430.7055-0.05860.1411.16520.2660.7999-6.132-13.6124-19.3049
42.61110.37420.3915.1082-0.44713.2796-0.09660.5391-0.4428-0.2613-0.0486-0.29460.23210.42250.15050.38740.07730.10360.5368-0.05180.58-14.8405-28.5896-9.1215
56.7789-1.73820.68513.0156-1.13844.64350.54662.23290.422-1.3439-0.46720.0019-0.1250.0058-0.06041.0491-0.0347-0.12531.15460.00430.6749-30.5435-20.612-32.3269
61.38971.3507-1.43565.9666-0.97413.1795-0.26240.93080.4517-1.54030.458-0.51270.39120.6446-0.21370.8484-0.1718-0.16541.2529-0.03430.8166-30.926-19.5285-25.547
74.7154-0.5820.3592.9631.39966.43010.20061.29890.1906-2.0243-0.22821.347-0.5242-0.26010.0170.9988-0.1535-0.32611.4550.12570.7562-41.6902-20.1783-33.5768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 87 )
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 180 )
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 266 )
5X-RAY DIFFRACTION5chain 'A' and (resid 267 through 317 )
6X-RAY DIFFRACTION6chain 'A' and (resid 318 through 362 )
7X-RAY DIFFRACTION7chain 'A' and (resid 363 through 385 )

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