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- PDB-6mr6: E. coli cysteine desulfurase SufS H55A with a cysteine persulfide... -

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Basic information

Entry
Database: PDB / ID: 6mr6
TitleE. coli cysteine desulfurase SufS H55A with a cysteine persulfide intermediate
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / cysteine desulfurase / SufS / persulfide
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
PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.019 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: Biochemistry / Year: 2019
Title: Structural Evidence for Dimer-Interface-Driven Regulation of the Type II Cysteine Desulfurase, SufS.
Authors: Dunkle, J.A. / Bruno, M.R. / Outten, F.W. / Frantom, P.A.
History
DepositionOct 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 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.title / _citation.year / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)46,0742
Polymers45,8271
Non-polymers2471
Water2,594144
1
A: Cysteine desulfurase
hetero molecules

A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1494
Polymers91,6542
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7740 Å2
ΔGint-38 kcal/mol
Surface area27200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.016, 127.016, 133.687
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-682-

HOH

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Components

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


Mass: 45827.176 Da / Num. of mol.: 1 / Mutation: H55A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: sufS, csdB, ynhB, b1680, JW1670 / Plasmid: pET21 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 5.88 Å3/Da / Density % sol: 79.09 % / Mosaicity: 0.66 °
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: 2.019→50 Å / Num. obs: 69593 / % possible obs: 96.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.05 / Rrim(I) all: 0.136 / Χ2: 1.991 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.02-2.0561.13534500.5990.4631.2310.52797.2
2.05-2.095.21.03634870.5460.4781.1471.12897.7
2.09-2.136.50.75434750.770.2950.8120.65398.9
2.13-2.186.60.66335230.8210.2580.7130.69899
2.18-2.226.40.57935210.860.2290.6240.7498.7
2.22-2.274.60.57834480.8260.2860.651.89796.6
2.27-2.336.20.4435120.8890.1770.4761.12898.8
2.33-2.396.20.3635190.9280.1440.3891.18798.5
2.39-2.476.20.31435090.9430.1250.3391.23198.7
2.47-2.545.80.27334330.9530.1090.2961.54896
2.54-2.646.70.23433070.9670.0870.2511.72291.9
2.64-2.746.90.21935050.9750.0830.2352.00898.2
2.74-2.877.10.17935120.9820.0660.1912.18498.1
2.87-3.0270.14435390.9880.0540.1552.49397.7
3.02-3.216.80.1235190.990.0460.1292.80897.6
3.21-3.456.20.135120.9920.0410.1093.42296.9
3.45-3.85.80.08232690.9930.0330.0893.79689.9
3.8-4.356.50.07134990.9950.0280.0773.95895.1
4.35-5.486.80.06135350.9960.0230.0663.60395.3
5.48-506.60.04535190.9970.0180.0492.63389.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
PHENIX1.14_3211refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JF9

1jf9


Resolution: 2.019→44.907 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.15
RfactorNum. reflection% reflection
Rfree0.2015 2013 2.9 %
Rwork0.1856 --
obs0.186 69469 96.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.82 Å2 / Biso mean: 31.034 Å2 / Biso min: 12.53 Å2
Refinement stepCycle: final / Resolution: 2.019→44.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 22 144 3281
Biso mean--26.65 32.85 -
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 (%)
2.0195-2.070.28321370.29094749488697
2.07-2.12590.24211540.24154821497598
2.1259-2.18850.26111390.21794884502399
2.1885-2.25910.2761370.25184752488996
2.2591-2.33990.20521420.21264864500698
2.3399-2.43360.23031430.2034919506299
2.4336-2.54430.22141500.2014773492397
2.5443-2.67840.23251370.1934666480394
2.6784-2.84620.22091410.19334894503598
2.8462-3.06590.16621460.18754874502098
3.0659-3.37440.20891500.18624875502597
3.3744-3.86240.19051380.16884636477492
3.8624-4.86530.1641520.15074870502295
4.8653-44.9180.18271470.16364879502692

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