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- PDB-6o13: E. coli cysteine desulfurase SufS H123A with a Cys-ketimine inter... -

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Basic information

Entry
Database: PDB / ID: 6o13
TitleE. coli cysteine desulfurase SufS H123A with a Cys-ketimine intermediate
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / LYASE / cysteine desulfurase / SufS / persulfide / PLP
Function / homology
Function and homology information


selenium compound metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / sulfur compound metabolic process / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly ...selenium compound metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / sulfur compound metabolic process / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly / pyridoxal phosphate binding / hydrolase activity / protein homodimerization activity / cytoplasm
Similarity search - Function
Cysteine desulfurase, SufS / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / 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, SufS / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / 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
Cys-ketimine / Cysteine desulfurase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.203 Å
AuthorsDunkle, J.A. / Frantom, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM112919 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Direct observation of intermediates in the SufS cysteine desulfurase reaction reveals functional roles of conserved active-site residues.
Authors: Blahut, M. / Wise, C.E. / Bruno, M.R. / Dong, G. / Makris, T.M. / Frantom, P.A. / Dunkle, J.A. / Outten, F.W.
History
DepositionFeb 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7993
Polymers44,4141
Non-polymers3862
Water1,60389
1
A: Cysteine desulfurase
hetero molecules

A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5996
Polymers88,8272
Non-polymers7714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7090 Å2
ΔGint-63 kcal/mol
Surface area27050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.012, 126.012, 137.214
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-644-

HOH

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Components

#1: Protein Cysteine desulfurase / Selenocysteine beta-lyase / SCL / Selenocysteine lyase / Selenocysteine reductase


Mass: 44413.523 Da / Num. of mol.: 1 / Mutation: H123A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: sufS, csdB, ynhB, b1680, JW1670 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P77444, cysteine desulfurase, selenocysteine lyase
#2: Chemical ChemComp-CKT / Cys-ketimine / (2Z)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-sulfanylpropanoic acid


Mass: 350.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 89 / 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: 6.13 Å3/Da / Density % sol: 79.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 4-4.5 M sodium chloride, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→56.354 Å / Num. obs: 56346 / % possible obs: 99.9 % / Redundancy: 14.821 % / Biso Wilson estimate: 67.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.117 / Χ2: 1.018 / Net I/σ(I): 12.71 / Num. measured all: 835082
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
2.2-2.3415.0962.0481.14134946898089390.612.11999.5
2.34-2.514.1021.2511.92119205845484530.7851.297100
2.5-2.715.5740.664.06123005789878980.9350.682100
2.7-2.9515.5090.3417.97112841727672760.9840.352100
2.95-3.314.9680.16914.8799147662566240.9950.175100
3.3-3.8113.9840.10123.3482354588958890.9970.104100
3.81-4.6715.3190.08831.6676717500850080.9970.091100
4.67-6.5914.2290.08932.6556191395139490.9970.09399.9
6.59-56.35413.280.06633.0830676231723100.9980.06899.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JF9

1jf9


Resolution: 2.203→56.354 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1986 1995 3.54 %
Rwork0.1873 102873 -
obs0.1877 56316 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.98 Å2 / Biso mean: 65.7185 Å2 / Biso min: 45.68 Å2
Refinement stepCycle: final / Resolution: 2.203→56.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 23 89 3226
Biso mean--60.75 67.24 -
Num. residues----405
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2027-2.23060.36141410.35233687382898
2.2306-2.25990.35181470.326338483995100
2.2599-2.29090.33491450.313938283973100
2.2909-2.32360.30611350.307337873922100
2.3236-2.35830.30491230.293338453968100
2.3583-2.39510.32281700.290937683938100
2.3951-2.43440.29621450.285138043949100
2.4344-2.47640.31081240.285538403964100
2.4764-2.52140.25961600.296538203980100
2.5214-2.56990.33831260.279338123938100
2.5699-2.62240.27691350.265438273962100
2.6224-2.67940.27811170.23838193936100
2.6794-2.74170.24071550.231138243979100
2.7417-2.81030.24031590.212137513910100
2.8103-2.88620.24031240.21938193943100
2.8862-2.97120.2471140.218838643978100
2.9712-3.06710.23891520.228237903942100
3.0671-3.17670.25781420.224538253967100
3.1767-3.30380.23851390.209638033942100
3.3038-3.45420.22871350.204238233958100
3.4542-3.63630.19581420.196838253967100
3.6363-3.8640.18161380.173738163954100
3.864-4.16230.18371310.164738133944100
4.1623-4.5810.14171390.142738213960100
4.581-5.24350.17421370.146838193956100
5.2435-6.60460.14591490.166937963945100
6.6046-56.37270.14531500.138337993949100

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