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- PDB-5wt2: NifS from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 5wt2
TitleNifS 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 / PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase IscS
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsFujishiro, T. / Takahashi, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS15H04472 Japan
JSPS15H06085 Japan
The Sumitomo Foundation163037 Japan
CitationJournal: Febs J. / Year: 2019
Title: Snapshots of PLP-substrate and PLP-product external aldimines as intermediates in two types of cysteine desulfurase enzymes.
Authors: Nakamura, R. / Hikita, M. / Ogawa, S. / Takahashi, Y. / Fujishiro, T.
History
DepositionDec 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / 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.title / _citation.year
Revision 1.2Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 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

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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)44,4684
Polymers44,1251
Non-polymers3433
Water1,31573
1
A: Cysteine desulfurase IscS
hetero molecules

A: Cysteine desulfurase IscS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9368
Polymers88,2502
Non-polymers6856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7220 Å2
ΔGint-46 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.010, 103.010, 133.650
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 / NifS


Mass: 44125.230 Da / Num. of mol.: 1 / Mutation: V2L, 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


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


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


Mass: 18.015 Da / Num. of mol.: 73 / 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: 4.02 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES/NaOH, PEG 4000, glycerol, isopropanol

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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: 2.3→43.553 Å / Num. obs: 32281 / % possible obs: 98.45 % / Observed criterion σ(I): -3 / Redundancy: 7.44 % / Biso Wilson estimate: 48.88 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0739 / Rpim(I) all: 0.0209 / Rrim(I) all: 0.0769 / Χ2: 1.025 / Net I/σ(I): 24.34 / Num. measured all: 448717 / Scaling rejects: 3318
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 7.614 % / Rmerge(I) obs: 0.8207 / Mean I/σ(I) obs: 3.78 / Num. measured obs: 46203 / Num. possible: 7306 / Num. unique obs: 3195 / CC1/2: 0.97 / Rpim(I) all: 0.2234 / Rrim(I) all: 0.851 / % possible all: 99.72

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ECX

1ecx


Resolution: 2.301→43.553 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2393 1604 5 %
Rwork0.2153 30492 -
obs0.2165 32088 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.67 Å2 / Biso mean: 81.4879 Å2 / Biso min: 29.05 Å2
Refinement stepCycle: final / Resolution: 2.301→43.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 20 73 2838
Biso mean--59.1 60.09 -
Num. residues----355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032814
X-RAY DIFFRACTIONf_angle_d0.6243811
X-RAY DIFFRACTIONf_chiral_restr0.046439
X-RAY DIFFRACTIONf_plane_restr0.004489
X-RAY DIFFRACTIONf_dihedral_angle_d20.0181686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3008-2.37510.34521600.339127593194100
2.3751-2.460.33481440.291927532897100
2.46-2.55850.3081470.281627812928100
2.5585-2.67490.30841440.272627362880100
2.6749-2.81590.26511450.24627632908100
2.8159-2.99230.29281460.25062766291299
2.9923-3.22320.29491460.25352779292599
3.2232-3.54750.26821470.2242783293099
3.5475-4.06050.2161470.19272791293899
4.0605-5.11450.19121490.17062829297898
5.1145-43.56060.19741440.18962752289691
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)
13.2834-0.13570.68223.0148-0.36684.2968-0.08181.0142-0.10810.2089-0.079-0.3313-0.08650.7980.12130.2454-0.02030.01330.6569-0.01530.5237-16.6287-25.2025-5.8391
22.7986-0.1629-0.85252.76220.2732.81430.0511.46170.0666-0.1975-0.2127-0.6847-0.26371.20090.1980.2664-0.0950.10551.32750.10810.6226-10.5249-22.1175-14.2852
34.8598-0.79580.79534.57810.8794.05790.08132.19260.2249-1.2031-0.25320.2119-0.29290.05220.06180.7101-0.0308-0.09521.7477-0.05660.6157-32.4749-22.8514-29.9312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 116 )A2 - 116
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 259 )A117 - 259
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 379 )A260 - 379

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