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- PDB-5wt5: L-homocysteine-bound NifS from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 5wt5
TitleL-homocysteine-bound 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
2-AMINO-4-MERCAPTO-BUTYRIC ACID / ISOPROPYL ALCOHOL / Cysteine desulfurase IscS
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFujishiro, T. / 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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
Revision 1.3Mar 6, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase IscS
B: Cysteine desulfurase IscS
C: Cysteine desulfurase IscS
D: Cysteine desulfurase IscS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,0149
Polymers177,4134
Non-polymers6015
Water13,854769
1
A: Cysteine desulfurase IscS
B: Cysteine desulfurase IscS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0375
Polymers88,7072
Non-polymers3303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-29 kcal/mol
Surface area26600 Å2
MethodPISA
2
C: Cysteine desulfurase IscS
D: Cysteine desulfurase IscS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9774
Polymers88,7072
Non-polymers2702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-30 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.440, 102.320, 132.050
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cysteine desulfurase IscS / NifS


Mass: 44353.348 Da / Num. of mol.: 4 / 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-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H9NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 769 / 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: 3.9 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HEPES/NaOH, PEG 4000, glycerol, isopropanol, L-homocysteine

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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: 1.897→47.782 Å / Num. obs: 221285 / % possible obs: 99.89 % / Redundancy: 3.7 % / Biso Wilson estimate: 29.91 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.0753 / Rpim(I) all: 0.04564 / Net I/σ(I): 11.91
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7912 / Mean I/σ(I) obs: 1.7 / Num. unique all: 21290 / CC1/2: 0.529 / Rpim(I) all: 0.4727 / % possible all: 99.76

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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: 1.9→47.782 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 10789 5.04 %
Rwork0.1836 --
obs0.1847 213980 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→47.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11308 0 36 769 12113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0211551
X-RAY DIFFRACTIONf_angle_d1.77515648
X-RAY DIFFRACTIONf_dihedral_angle_d22.3866927
X-RAY DIFFRACTIONf_chiral_restr0.1121804
X-RAY DIFFRACTIONf_plane_restr0.0122008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.9-1.92160.226311070.1971671121249100
1.9216-1.94420.23843650.19586693100
1.9442-1.96790.23113950.19086729100
1.9679-1.99280.22413730.19056641100
1.9928-2.0190.20523490.17996812100
2.019-2.04670.18173360.16836782100
2.0467-2.07590.19383560.166656100
2.0759-2.10690.18693960.16066779100
2.1069-2.13990.17243490.15776761100
2.1399-2.17490.18293670.15416776100
2.1749-2.21240.18553700.15036716100
2.2124-2.25270.17453820.14656737100
2.2527-2.2960.16723150.15156781100
2.296-2.34290.18293850.14686750100
2.3429-2.39380.15543250.14316806100
2.3938-2.44950.18533470.14736810100
2.4495-2.51070.18423820.15676714100
2.5107-2.57860.18763420.15536794100
2.5786-2.65450.17683370.15846794100
2.6545-2.74020.19693460.17356789100
2.7402-2.83810.22953290.18316857100
2.8381-2.95170.21473140.20256760100
2.9517-3.0860.20134070.19396734100
3.086-3.24870.2393480.22146769100
3.2487-3.45220.24073670.22156846100
3.4522-3.71860.2624240.21976761100
3.7186-4.09270.19773340.19136828100
4.0927-4.68440.22043950.18886793100
4.6844-5.90020.2043530.17996852100
5.9002-47.79660.19793530.1765694499
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)
11.76850.8152-2.31011.1552-1.53176.12690.05990.01470.06430.00170.02050.2184-0.1753-0.21-0.1420.1220.0139-0.0210.1589-0.02330.2189-9.11596.94614.0795
21.6313-0.2969-0.02631.60640.48041.0920.00570.164-0.2467-0.26410.0044-0.11570.22220.0521-0.0020.2774-0.01030.04970.1826-0.02310.23097.0965-8.81724.1498
31.87550.5865-0.71122.51-0.74134.065-0.12950.50970.1214-0.81050.0294-0.3910.01410.2230.11430.4250.02980.0860.30580.0270.34981.468912.681-11.3349
40.67240.3729-0.92530.8594-0.80693.40950.0334-0.02890.2043-0.00570.01730.0304-0.1976-0.099-0.11810.20280.01310.01370.1428-0.0260.23750.795517.645618.5095
52.3256-0.57960.64871.8133-0.43151.8680.0195-0.3782-0.05080.1568-0.0136-0.23140.07390.2409-0.00480.19-0.0220.01340.2816-0.00590.224617.02362.920830.0157
63.16761.0156-2.14712.1416-1.24775.77940.0449-0.807-0.15640.4885-0.18460.0370.12480.20420.13510.26180.04470.00460.392-0.03270.2934-5.29757.793944.0674
70.86430.05580.89010.65520.74524.5549-0.01810.0643-0.3236-0.07420.0689-0.02460.20830.2836-0.06470.20890.00570.01710.1660.01190.277650.3242-50.0545-47.6906
82.4806-0.1848-0.5621.95310.18722.27070.0042-0.32620.09230.15940.0070.2383-0.131-0.3058-0.00320.1908-0.0050.02770.26650.01740.21734.2802-35.3102-36.2316
92.98680.51231.49581.32110.23994.40570.0216-0.7520.16440.371-0.11120.0742-0.1629-0.14560.10050.24410.04190.05950.39890.01270.302254.3856-41.1027-23.5618
101.97140.82892.95760.51811.79026.3448-0.2468-0.50030.54290.4667-0.0511-0.2246-0.89970.46490.16420.4784-0.065-0.06370.6999-0.02860.42667.5082-36.3908-15.4076
110.81060.4280.76071.03711.12433.15290.0715-0.0363-0.1277-0.02060.0058-0.29040.22940.0933-0.12330.22580.01340.04740.26570.01740.32260.1542-39.2543-51.8805
122.5444-0.2640.80541.971-0.51231.9286-0.05280.20810.3781-0.2115-0.00420.1195-0.3431-0.03310.06090.2732-0.01420.02450.20980.03080.249245.5201-24.2614-61.6476
135.57112.5952.11274.98342.14195.1897-0.21320.7707-0.068-0.58730.08230.3719-0.10780.04150.10940.40030.06720.05160.3642-0.04090.293447.4081-46.4491-80.3832
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 243 )
3X-RAY DIFFRACTION3chain 'A' and (resid 244 through 385 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 59 )
5X-RAY DIFFRACTION5chain 'B' and (resid 60 through 243 )
6X-RAY DIFFRACTION6chain 'B' and (resid 244 through 384 )
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 59 )
8X-RAY DIFFRACTION8chain 'C' and (resid 60 through 243 )
9X-RAY DIFFRACTION9chain 'C' and (resid 244 through 362 )
10X-RAY DIFFRACTION10chain 'C' and (resid 363 through 386 )
11X-RAY DIFFRACTION11chain 'D' and (resid 2 through 59 )
12X-RAY DIFFRACTION12chain 'D' and (resid 60 through 259 )
13X-RAY DIFFRACTION13chain 'D' and (resid 260 through 386 )

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