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- PDB-6mri: E. coli cysteine desulfurase SufS E250A with a cysteine persulfid... -

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Basic information

Entry
Database: PDB / ID: 6mri
TitleE. coli cysteine desulfurase SufS E250A 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: 2.62 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 12, 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)46,0832
Polymers45,8361
Non-polymers2471
Water1,49583
1
A: Cysteine desulfurase
hetero molecules

A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1674
Polymers91,6722
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7820 Å2
ΔGint-39 kcal/mol
Surface area27280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.730, 125.730, 138.550
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-665-

HOH

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Components

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


Mass: 45836.211 Da / Num. of mol.: 1 / Mutation: E250A
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.: 83 / 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: 5.97 Å3/Da / Density % sol: 79.41 %
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: Mar 30, 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: 2.62→60.675 Å / Num. obs: 31408 / % possible obs: 92.4 % / Redundancy: 7.044 % / Biso Wilson estimate: 57.804 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.157 / Rrim(I) all: 0.169 / Χ2: 1.028 / Net I/σ(I): 6.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.62-2.697.3980.6972.0923270.5920.75794.9
2.69-2.767.3820.62.4122790.7030.65194.4
2.76-2.847.4820.5272.922210.6630.57294.3
2.84-2.937.430.4553.3321580.7760.49494.1
2.93-3.037.3470.3554.320440.840.38693.4
3.03-3.137.2670.3114.9620140.8840.33793.6
3.13-3.257.1950.2715.5219070.9240.29393
3.25-3.386.9260.2276.5718700.9290.24693
3.38-3.536.8180.2047.5917600.9530.22191.4
3.53-3.716.0990.188.0316940.970.19692.2
3.71-3.916.4710.1639.0116280.9690.17792.3
3.91-4.147.0160.1629.9715210.9770.17592
4.14-4.436.9470.13910.8714400.9840.14991.6
4.43-4.786.9170.13111.3113430.9820.14191.2
4.78-5.246.8580.1211.3112340.9890.12990.7
5.24-5.866.990.11211.3511090.9930.1289.6
5.86-6.766.80.10311.299720.9910.1188.6
6.76-8.296.4780.0811.518280.9950.08686.8
8.29-11.727.090.06912.696680.9970.07387.8
11.72-60.6756.3170.04911.763910.9980.05285.7

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1jf9


Resolution: 2.62→60.675 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 1998 6.37 %
Rwork0.1844 29345 -
obs0.1867 31343 92.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.93 Å2 / Biso mean: 54.1989 Å2 / Biso min: 34.7 Å2
Refinement stepCycle: final / Resolution: 2.62→60.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 22 83 3221
Biso mean--52.47 56.96 -
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 (%)
2.62-2.68560.33021430.27332084222794
2.6856-2.75820.28661410.25452085222694
2.7582-2.83930.28771450.24012112225794
2.8393-2.9310.2971420.2392101224394
2.931-3.03570.26461430.22542084222793
3.0357-3.15730.28591430.23562108225193
3.1573-3.3010.28821430.2152104224793
3.301-3.4750.2421400.19782066220692
3.475-3.69270.19511420.18162087222992
3.6927-3.97770.21941420.16112085222792
3.9777-4.37790.16791420.14942082222492
4.3779-5.01120.17561440.14712113225791
5.0112-6.31250.20511420.17192089223190
6.3125-60.69090.1951460.17242145229187

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