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- PDB-6o11: E. coli cysteine desulfurase SufS C364A with a Cys-aldimine inter... -

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Basic information

Entry
Database: PDB / ID: 6o11
TitleE. coli cysteine desulfurase SufS C364A with a Cys-aldimine 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
Chem-C6P / Cysteine desulfurase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 1.0Jun 26, 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
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

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Assembly

Deposited unit
A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8363
Polymers44,4491
Non-polymers3882
Water1,72996
1
A: Cysteine desulfurase
hetero molecules

A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6736
Polymers88,8972
Non-polymers7764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6940 Å2
ΔGint-65 kcal/mol
Surface area26840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.426, 126.426, 67.087
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-603-

HOH

21A-667-

HOH

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Components

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


Mass: 44448.531 Da / Num. of mol.: 1 / Mutation: C364A
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-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20-30% w/v PEG3350, 0.1 M Tris-HCl, 0.2 M magnesium chloride

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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 25, 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: 1.84→89.397 Å / Num. obs: 46852 / % possible obs: 98.2 % / Redundancy: 12.079 % / Biso Wilson estimate: 50.724 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.085 / Χ2: 1.018 / Net I/σ(I): 15.51 / Num. measured all: 565938
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.84-1.957.5251.8670.7667820.496289.1
1.95-2.0911.6510.92.2871030.8420.94199.4
2.09-2.2513.6730.485.6666850.9620.499100
2.25-2.4713.2650.26510.6961610.9880.275100
2.47-2.7612.9730.14617.8155920.9960.152100
2.76-3.1813.5580.08827.9249820.9980.091100
3.18-3.912.3110.06735.0942460.9980.069100
3.9-5.5113.2550.0641.3133410.9980.062100
5.51-89.39711.4140.06438.7619600.9970.06799.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3211refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JF9

1jf9


Resolution: 1.84→37.198 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.98
RfactorNum. reflection% reflection
Rfree0.2162 3728 4.24 %
Rwork0.1838 --
obs0.1851 46703 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.71 Å2 / Biso mean: 48.7749 Å2 / Biso min: 33.88 Å2
Refinement stepCycle: final / Resolution: 1.84→37.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 0 23 96 3245
Biso mean--40.22 49.43 -
Num. residues----406
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 (%)
1.84-1.86320.36851040.34812230233468
1.8632-1.88780.36531150.34262621273683
1.8878-1.91360.33451290.32792837296689
1.9136-1.9410.34921300.30053000313094
1.941-1.96990.33591390.29573095323496
1.9699-2.00070.36791370.263731593296100
2.0007-2.03350.25961440.265732283372100
2.0335-2.06860.29051420.25631713313100
2.0686-2.10620.27921410.253132283369100
2.1062-2.14670.26031410.242731773318100
2.1467-2.19050.24021420.229531913333100
2.1905-2.23810.24881450.217432203365100
2.2381-2.29020.22891460.211431543300100
2.2902-2.34740.2551400.213432023342100
2.3474-2.41090.2791500.208332003350100
2.4109-2.48180.28771400.205332243364100
2.4818-2.56190.2531390.206631893328100
2.5619-2.65350.22151460.205331733319100
2.6535-2.75970.19681420.201932103352100
2.7597-2.88520.23671440.203431953339100
2.8852-3.03730.21181390.199532013340100
3.0373-3.22750.24081470.202931983345100
3.2275-3.47650.23131410.193131783319100
3.4765-3.8260.1971390.175532093348100
3.826-4.37890.17851300.152732103340100
4.3789-5.51410.16571440.13931913335100
5.5141-37.20560.18731320.140432163348100

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