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- PDB-6o12: E. coli cysteine desulfurase SufS H123A -

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Basic information

Entry
Database: PDB / ID: 6o12
TitleE. coli cysteine desulfurase SufS H123A
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 / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / sulfur compound 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 / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / sulfur compound 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
PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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)44,6963
Polymers44,4141
Non-polymers2832
Water1,54986
1
A: Cysteine desulfurase
hetero molecules

A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3926
Polymers88,8272
Non-polymers5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8140 Å2
ΔGint-63 kcal/mol
Surface area26950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.280, 127.280, 134.163
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-646-

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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#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.: 86 / 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: 6.12 Å3/Da / Density % sol: 79.89 % / Mosaicity: 0.373 °
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: Jun 7, 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: 2.05→50 Å / Num. obs: 69256 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.068 / Rrim(I) all: 0.175 / Χ2: 1.578 / Net I/σ(I): 6.2 / Num. measured all: 463185
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.096.12.55934080.4571.1672.8220.64499.8
2.09-2.126.92.02234450.3990.8432.1950.427100
2.12-2.167.11.55433900.5350.641.6840.435100
2.16-2.217.21.38134030.5630.5641.4940.461100
2.21-2.266.11.09334210.8140.5021.2071.02299.7
2.26-2.316.80.92634310.7390.3891.0060.521100
2.31-2.3770.64834380.8470.2660.7020.534100
2.37-2.436.90.54834160.8690.2260.5940.57899.9
2.43-2.56.50.45634320.8930.1920.4960.645100
2.5-2.585.90.35234080.9210.1520.3840.76199.4
2.58-2.687.10.3334460.9340.1340.3560.967100
2.68-2.787.40.27634500.9610.110.2981.133100
2.78-2.917.40.22734660.970.0910.2451.43999.9
2.91-3.067.20.18634440.9790.0750.2012.00199.8
3.06-3.256.90.1634820.9830.0660.1732.576100
3.25-3.516.40.12634910.9870.0550.1383.251100
3.51-3.865.50.09434660.9910.0430.1033.68598.9
3.86-4.426.60.08235220.9930.0350.0894.16999.9
4.42-5.566.50.0735670.9950.0290.0763.8499.9
5.56-506.20.05537300.9970.0230.062.9698.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JF9

1jf9


Resolution: 2.05→43.402 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.6
RfactorNum. reflection% reflection
Rfree0.2159 2004 2.91 %
Rwork0.1945 --
obs0.1951 68944 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.94 Å2 / Biso mean: 39.5874 Å2 / Biso min: 23.87 Å2
Refinement stepCycle: final / Resolution: 2.05→43.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 23 86 3223
Biso mean--44.44 39.43 -
Num. residues----405
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0503-2.10160.39271450.36634412455793
2.1016-2.15840.30341330.296647474880100
2.1584-2.22190.29361420.262747524894100
2.2219-2.29370.30021480.27954693484199
2.2937-2.37560.26141410.2447554896100
2.3756-2.47070.24671340.221247804914100
2.4707-2.58320.24571590.212347324891100
2.5832-2.71940.26351360.207448024938100
2.7194-2.88970.21131370.207448074944100
2.8897-3.11280.20871510.204447984949100
3.1128-3.42590.21011390.197748384977100
3.4259-3.92130.18831420.17794813495599
3.9213-4.93940.18891470.149149125059100
4.9394-43.41160.17681500.16315099524999

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