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- PDB-6mre: E. coli cysteine desulfurase SufS R92A with a cysteine persulfide... -

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Basic information

Entry
Database: PDB / ID: 6mre
TitleE. coli cysteine desulfurase SufS R92A 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: 2.5 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)46,0552
Polymers45,8081
Non-polymers2471
Water2,540141
1
A: Cysteine desulfurase
hetero molecules

A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1114
Polymers91,6162
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7510 Å2
ΔGint-43 kcal/mol
Surface area27210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.980, 126.980, 135.220
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: 45808.129 Da / Num. of mol.: 1 / Mutation: R92A
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.: 141 / 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: 5.95 Å3/Da / Density % sol: 79.33 %
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: 2.5→46.282 Å / Num. obs: 38840 / % possible obs: 100 % / Redundancy: 12.786 % / Biso Wilson estimate: 63.478 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.149 / Rrim(I) all: 0.156 / Χ2: 1.045 / Net I/σ(I): 15.97 / Num. measured all: 496623 / Scaling rejects: 46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.5612.041.5672.0928010.6831.63699.9
2.56-2.6413.3561.3822.6527550.7441.437100
2.64-2.7114.1271.1363.3526960.8241.179100
2.71-2.814.1340.9544.1725940.8580.99100
2.8-2.8913.8840.7935.5725450.9230.824100
2.89-2.9913.8650.6377.7324420.9710.661100
2.99-3.113.7230.49810.3223640.9820.518100
3.1-3.2313.5780.40712.0622720.9890.423100
3.23-3.3713.130.29415.5121990.9930.306100
3.37-3.5412.5240.20419.321060.9950.213100
3.54-3.7310.950.1421.9820060.9960.14799.9
3.73-3.9512.2230.11825.7619010.9970.123100
3.95-4.2312.6240.09229.7418010.9980.096100
4.23-4.5612.2690.07732.7616720.9970.081100
4.56-511.9960.07333.7915540.9970.076100
5-5.5911.7420.06932.7314070.9980.072100
5.59-6.4511.2890.06931.9612680.9980.072100
6.45-7.919.8180.05632.1510730.9980.05999.6
7.91-11.1811.1310.0538.688650.9980.053100
11.18-46.28210.6630.04937.215190.9990.05199.6

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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: 2.5→46.282 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.42
RfactorNum. reflection% reflection
Rfree0.199 1992 5.13 %
Rwork0.1779 --
obs0.179 38827 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.31 Å2 / Biso mean: 54.7547 Å2 / Biso min: 31.96 Å2
Refinement stepCycle: final / Resolution: 2.5→46.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 23 141 3278
Biso mean--49.32 59.78 -
Num. residues----405
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.56250.33481330.295925862719
2.5625-2.63180.28841410.270925702711
2.6318-2.70920.30691500.263825912741
2.7092-2.79670.32391380.258825742712
2.7967-2.89660.3051480.242126042752
2.8966-3.01260.25541390.231125912730
3.0126-3.14960.25011440.232626162760
3.1496-3.31570.22071430.209826172760
3.3157-3.52330.19231340.186926142748
3.5233-3.79520.17491420.15326192761
3.7952-4.1770.18461420.15326432785
4.177-4.78080.15571460.129226692815
4.7808-6.02130.17181400.154127052845
6.0213-46.29010.15831520.157628362988

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