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- PDB-6mrh: E. coli cysteine desulfurase SufS E96A with a cysteine persulfide... -

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Basic information

Entry
Database: PDB / ID: 6mrh
TitleE. coli cysteine desulfurase SufS E96A 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: 2.02 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
Water2,126118
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 area7730 Å2
ΔGint-36 kcal/mol
Surface area26800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.974, 125.974, 136.952
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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: E96A
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 / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 5.93 Å3/Da / Density % sol: 79.25 % / Mosaicity: 0.392 °
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: 2.02→50 Å / Num. obs: 72610 / % possible obs: 99.4 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.037 / Rrim(I) all: 0.104 / Χ2: 1.455 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.02-2.0571.40132480.4970.5671.5160.44290.5
2.05-2.097.81.09935970.6960.4211.1790.457100
2.09-2.138.10.92935860.7860.3490.9930.486100
2.13-2.188.20.76536240.8170.2850.8180.513100
2.18-2.228.10.66336010.870.2490.7090.5599.8
2.22-2.277.60.51735630.870.2020.5560.77299.1
2.27-2.3380.41736010.9350.1570.4460.66799.9
2.33-2.397.90.3536100.950.1320.3750.75599.8
2.39-2.477.60.29635950.9610.1130.3170.82999.9
2.47-2.5470.23936220.970.0960.2580.9699.9
2.54-2.647.20.19736390.9770.0780.2131.108100
2.64-2.748.30.17736400.9840.0650.1881.331100
2.74-2.878.30.15336260.9880.0560.1631.503100
2.87-3.0280.12636430.9910.0470.1341.8699.9
3.02-3.217.80.10536500.9920.040.1122.261100
3.21-3.457.30.08636640.9950.0340.0922.63499.8
3.45-3.86.40.06736840.9950.0290.0732.9599.6
3.8-4.357.80.06137180.9960.0240.0663.204100
4.35-5.487.60.05737540.9970.0220.0613.25799.8
5.48-5070.04839450.9980.0190.0522.66599.6

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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: 2.02→43.506 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.77
RfactorNum. reflection% reflection
Rfree0.2118 2002 2.76 %
Rwork0.194 --
obs0.1945 72510 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.67 Å2 / Biso mean: 40.4341 Å2 / Biso min: 25.49 Å2
Refinement stepCycle: final / Resolution: 2.02→43.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 22 118 3256
Biso mean--35.71 42.04 -
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 (%)
2.0184-2.06880.30071490.29194821497097
2.0688-2.12480.2421440.241349685112100
2.1248-2.18730.24361330.228650065139100
2.1873-2.25790.22661420.23594945508799
2.2579-2.33860.23781350.213849985133100
2.3386-2.43220.22521480.208949725120100
2.4322-2.54290.2231480.210650135161100
2.5429-2.6770.22121390.207750305169100
2.677-2.84460.24861530.210150255178100
2.8446-3.06420.2361290.211650405169100
3.0642-3.37250.23371400.203750725212100
3.3725-3.86020.20621410.18750985239100
3.8602-4.86250.18051480.162151375285100
4.8625-43.51560.18621530.175153835536100

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