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- PDB-8d8s: SufS from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 8d8s
TitleSufS from Staphylococcus aureus
ComponentsCysteine desulfurase
KeywordsBIOSYNTHETIC PROTEIN / SufS / cysteine desulfurase / iron-sulfur cluster biosynthesis
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding / lyase activity
Similarity search - Function
Cysteine desulfurase, SufS / Cysteine desulfurase / Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Probable cysteine desulfurase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.388 Å
AuthorsMorrison, C.N. / Boncella, A.E. / Lunin, V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Omega / Year: 2022
Title: Structural and Biochemical Characterization of Staphylococcus aureus Cysteine Desulfurase Complex SufSU.
Authors: Hudspeth, J.D. / Boncella, A.E. / Sabo, E.T. / Andrews, T. / Boyd, J.M. / Morrison, C.N.
History
DepositionJun 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 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

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Assembly

Deposited unit
A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6894
Polymers46,5031
Non-polymers1863
Water6,648369
1
A: Cysteine desulfurase
hetero molecules

A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3798
Polymers93,0062
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7740 Å2
ΔGint-10 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.853, 93.853, 101.461
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cysteine desulfurase /


Mass: 46503.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: sufS / Production host: Escherichia coli (E. coli) / References: UniProt: X5E2K8, cysteine desulfurase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.35 / Details: Tris, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.34 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Nov 16, 2021 / Details: Helios MX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 1.388→31.737 Å / Num. obs: 104403 / % possible obs: 100 % / Redundancy: 22.6 % / Rmerge(I) obs: 0.015 / Rpim(I) all: 0.015 / Rrim(I) all: 0.021 / Net I/σ(I): 22.8
Reflection shellResolution: 1.388→1.41 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4995 / Rpim(I) all: 0.415 / Rrim(I) all: 0.587 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
APEXdata reduction
APEXdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J8Q

5j8q


Resolution: 1.388→31.737 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.863 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.049 / ESU R Free: 0.051
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1911 2054 1.968 %
Rwork0.1679 102290 -
all0.168 --
obs-104344 99.863 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.802 Å2
Baniso -1Baniso -2Baniso -3
1--0.098 Å2-0.049 Å20 Å2
2---0.098 Å20 Å2
3---0.317 Å2
Refinement stepCycle: LAST / Resolution: 1.388→31.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 12 369 3653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0133445
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163218
X-RAY DIFFRACTIONr_angle_refined_deg2.0541.644684
X-RAY DIFFRACTIONr_angle_other_deg2.0231.5787423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1485434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99623.722180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75715582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8711515
X-RAY DIFFRACTIONr_chiral_restr0.10.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023980
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02773
X-RAY DIFFRACTIONr_nbd_refined0.2410.2724
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.23053
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21740
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21583
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2223
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1860.29
X-RAY DIFFRACTIONr_nbd_other0.1510.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.224
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0780.21
X-RAY DIFFRACTIONr_mcbond_it1.4031.6391705
X-RAY DIFFRACTIONr_mcbond_other1.3921.6371704
X-RAY DIFFRACTIONr_mcangle_it1.922.4572149
X-RAY DIFFRACTIONr_mcangle_other1.9242.4592150
X-RAY DIFFRACTIONr_scbond_it2.961.9811740
X-RAY DIFFRACTIONr_scbond_other2.9591.9821741
X-RAY DIFFRACTIONr_scangle_it4.3592.8452535
X-RAY DIFFRACTIONr_scangle_other4.3582.8462536
X-RAY DIFFRACTIONr_lrange_it4.95220.9963992
X-RAY DIFFRACTIONr_lrange_other4.8520.5563918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.388-1.4240.2591590.2557403X-RAY DIFFRACTION98.4379
1.424-1.4630.2581170.2297321X-RAY DIFFRACTION100
1.463-1.5050.2261430.2067124X-RAY DIFFRACTION100
1.505-1.5510.191320.1916892X-RAY DIFFRACTION100
1.551-1.6020.2351520.1936708X-RAY DIFFRACTION100
1.602-1.6580.204970.1816509X-RAY DIFFRACTION100
1.658-1.7210.2371060.1786311X-RAY DIFFRACTION100
1.721-1.7910.1841390.1816041X-RAY DIFFRACTION100
1.791-1.8710.214950.1775819X-RAY DIFFRACTION100
1.871-1.9620.2041340.1755508X-RAY DIFFRACTION99.9469
1.962-2.0680.1991160.1725283X-RAY DIFFRACTION99.9815
2.068-2.1930.201940.1645033X-RAY DIFFRACTION99.9805
2.193-2.3450.1671140.1554687X-RAY DIFFRACTION100
2.345-2.5320.163860.1454396X-RAY DIFFRACTION99.9777
2.532-2.7740.1921010.1514051X-RAY DIFFRACTION99.9278
2.774-3.1010.183810.1623668X-RAY DIFFRACTION99.9733
3.101-3.580.212820.1663258X-RAY DIFFRACTION100
3.58-4.3820.175430.142798X-RAY DIFFRACTION99.9648
4.382-6.1880.156440.1652204X-RAY DIFFRACTION100
6.188-31.7370.155190.1951276X-RAY DIFFRACTION99.0819

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