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- PDB-6efn: Structure of a RiPP maturase, SkfB -

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Basic information

Entry
Database: PDB / ID: 6efn
TitleStructure of a RiPP maturase, SkfB
ComponentsSporulation killing factor maturation protein SkfB
KeywordsOXIDOREDUCTASE / S-Adenosylmethinine radical enzyme / metalloenzyme / natural product / RiPP / metal binding protein
Function / homology
Function and homology information


Oxidoreductases; Catalysing the reaction X-H + Y-H = X-Y; With other, known, physiological acceptors / bacteriocin biosynthetic process / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding / cytoplasm
Similarity search - Function
Sporulation killing factor system, radical SAM maturase SkfB / MoaA/NifB/PqqE, iron-sulphur binding, conserved site / moaA / nifB / pqqE family signature. / 4Fe4S-binding SPASM domain / Iron-sulfur cluster-binding domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Sporulation killing factor maturation protein SkfB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.291 Å
AuthorsGrell, T.A.J. / Drennan, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1122374 United States
CitationJournal: J.Biol.Chem. / Year: 2018
Title: Structure of a RiPP maturase, SkfB
Authors: Grell, T.A.J. / Kincannon, W.M. / Bruender, N.A. / Blaesi, E.J. / Krebs, C. / Bandarian, V. / Drennan, C.L.
History
DepositionAug 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sporulation killing factor maturation protein SkfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9525
Polymers46,0021
Non-polymers9504
Water7,026390
1
A: Sporulation killing factor maturation protein SkfB
hetero molecules

A: Sporulation killing factor maturation protein SkfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,90510
Polymers92,0042
Non-polymers1,9008
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5110 Å2
ΔGint-96 kcal/mol
Surface area29970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.462, 83.110, 61.299
Angle α, β, γ (deg.)90.00, 94.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-504-

MG

21A-939-

HOH

31A-957-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sporulation killing factor maturation protein SkfB


Mass: 46002.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: skfB, ybcP, ybcQ, BSU01920 / Production host: Escherichia coli (E. coli)
References: UniProt: O31423, Oxidoreductases; Catalysing the reaction X-H + Y-H = X-Y; With other, known, physiological acceptors

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Non-polymers , 5 types, 394 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.25 M magnesium formate, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2013
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.291→42.574 Å / Num. obs: 92230 / % possible obs: 96.72 % / Redundancy: 5.6 % / Rsym value: 0.037 / Net I/σ(I): 43.6
Reflection shellResolution: 1.291→1.34 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.729 / Rsym value: 0.499 / % possible all: 76.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.291→42.574 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.6
RfactorNum. reflection% reflection
Rfree0.1685 9470 7.49 %
Rwork0.1425 --
obs0.1445 83737 66.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.291→42.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 40 390 3354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063362
X-RAY DIFFRACTIONf_angle_d0.9274622
X-RAY DIFFRACTIONf_dihedral_angle_d20.071254
X-RAY DIFFRACTIONf_chiral_restr0.08514
X-RAY DIFFRACTIONf_plane_restr0.006608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2907-1.30540.2787330.2676398X-RAY DIFFRACTION7
1.3054-1.32070.2509520.2182661X-RAY DIFFRACTION11
1.3207-1.33680.2196820.20921046X-RAY DIFFRACTION18
1.3368-1.35370.26391080.18781466X-RAY DIFFRACTION25
1.3537-1.37160.1951540.19151942X-RAY DIFFRACTION33
1.3716-1.39040.19731970.16982296X-RAY DIFFRACTION40
1.3904-1.41020.22261960.16722664X-RAY DIFFRACTION45
1.4102-1.43130.22592140.16492709X-RAY DIFFRACTION47
1.4313-1.45360.19692520.15822847X-RAY DIFFRACTION48
1.4536-1.47750.18662380.14822941X-RAY DIFFRACTION51
1.4775-1.50290.16792360.14083035X-RAY DIFFRACTION52
1.5029-1.53030.17782470.14323104X-RAY DIFFRACTION53
1.5303-1.55970.16442490.13873134X-RAY DIFFRACTION54
1.5597-1.59150.16652920.13293343X-RAY DIFFRACTION58
1.5915-1.62620.16262830.13163731X-RAY DIFFRACTION64
1.6262-1.6640.15913530.12844084X-RAY DIFFRACTION70
1.664-1.70560.16593810.1364379X-RAY DIFFRACTION75
1.7056-1.75170.16433970.13285226X-RAY DIFFRACTION90
1.7517-1.80330.16674570.13345549X-RAY DIFFRACTION95
1.8033-1.86150.16344190.1265645X-RAY DIFFRACTION96
1.8615-1.9280.15415000.13485653X-RAY DIFFRACTION97
1.928-2.00520.17784180.13425683X-RAY DIFFRACTION97
2.0052-2.09640.16564650.12825534X-RAY DIFFRACTION95
2.0964-2.2070.15784290.13715572X-RAY DIFFRACTION95
2.207-2.34520.15115170.13515767X-RAY DIFFRACTION99
2.3452-2.52630.17894390.14645777X-RAY DIFFRACTION99
2.5263-2.78050.1894690.16045760X-RAY DIFFRACTION98
2.7805-3.18270.19744570.15265566X-RAY DIFFRACTION96
3.1827-4.00940.16154620.14215761X-RAY DIFFRACTION99
4.0094-42.59720.15154740.14495676X-RAY DIFFRACTION97

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