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- PDB-5wt4: L-Cysteine-PLP intermediate of NifS from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 5wt4
TitleL-Cysteine-PLP 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
Chem-C6P / ISOPROPYL ALCOHOL / Cysteine desulfurase IscS
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsFujishiro, T. / Nakamura, R. / Takahashi, T.
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)44,5383
Polymers44,1251
Non-polymers4122
Water1629
1
A: Cysteine desulfurase IscS
hetero molecules

A: Cysteine desulfurase IscS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0756
Polymers88,2502
Non-polymers8254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5780 Å2
ΔGint-30 kcal/mol
Surface area26690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.170, 103.170, 133.620
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: 44125.230 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 / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-C6P / N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-CYSTEINE / 4-((1-CARBOXY-2-THIOL-ETHYLAMINO)-METHYL)-3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDINIUM


Mass: 352.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N2O7PS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.03 Å3/Da / Density % sol: 69.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES/NaOH, PEG4000, glycerol, isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2016
RadiationMonochromator: 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: 2.92→50 Å / Num. obs: 16036 / % possible obs: 97.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 66.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1082 / Net I/σ(I): 26.52
Reflection shellResolution: 2.92→3.024 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.9236 / Mean I/σ(I) obs: 3.59 / Num. unique all: 1579 / CC1/2: 0.908 / % possible all: 99.8

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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: 2.92→48.123 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.07
RfactorNum. reflection% reflection
Rfree0.2922 795 5 %
Rwork0.2677 --
obs0.269 15900 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.92→48.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 26 9 2810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012850
X-RAY DIFFRACTIONf_angle_d1.553860
X-RAY DIFFRACTIONf_dihedral_angle_d21.6271719
X-RAY DIFFRACTIONf_chiral_restr0.095446
X-RAY DIFFRACTIONf_plane_restr0.011496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.9201-3.1030.30271320.295424971575100
3.103-3.34250.37591310.32122510100
3.3425-3.67880.46091240.3838236093
3.6788-4.21080.361280.3048243395
4.2108-5.30410.22761350.21752564100
5.3041-48.12990.21341450.21282739100
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)
12.67011.18470.06934.0586-0.24055.5216-0.00620.723-0.51680.2669-0.0089-0.15570.41110.39660.13850.26870.09150.06710.4739-0.06540.5098-19.4783-30.5671-3.6831
28.07761.13290.01313.7620.01780.1849-0.17751.3346-0.1832-0.49780.1488-0.278-0.96941.0289-0.21680.7985-0.4572-0.02841.43380.39090.8788-7.7315-8.9524-16.5104
33.920.6383-1.59493.43720.25553.68770.01771.3962-0.1925-0.26970.164-0.5341-0.3011.1369-0.09490.3538-0.06130.1251.2321-0.05580.6441-8.9495-22.3264-13.6335
43.9607-1.04721.45683.9755-1.09025.60350.01791.95370.1749-1.5114-0.29180.11190.27010.05560.21510.72230.0019-0.04981.4294-0.05750.5579-29.0635-24.9642-26.0196
56.8988-3.697-1.68359.64694.01182.92050.98351.96021.9703-2.65010.01971.3783-0.9892-0.37660.0141.2307-0.2373-0.55882.36930.02610.1306-42.1216-20.5474-33.4765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 133 )
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 243 )
4X-RAY DIFFRACTION4chain 'A' and (resid 244 through 362 )
5X-RAY DIFFRACTION5chain 'A' and (resid 363 through 384 )

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