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- PDB-5wgg: Structural Insights into Thioether Bond Formation in the Biosynth... -

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Basic information

Entry
Database: PDB / ID: 5wgg
TitleStructural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides
Components
  • CteA
  • Radical SAM domain protein
KeywordsPEPTIDE BINDING PROTEIN / radical SAM binding / metalloprotein / SCIFF maturase / SPASM domain-containing
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Six-cysteine peptide SCIFF / Six-cysteine peptide SCIFF / SCIFF radical SAM maturase / Anaerobic sulphatase maturase, radical SAM / MoaA/NifB/PqqE, iron-sulphur binding, conserved site / moaA / nifB / pqqE family signature. / 4Fe4S-binding SPASM domain / Iron-sulfur cluster-binding domain / 4Fe-4S single cluster domain / Radical SAM superfamily ...Six-cysteine peptide SCIFF / Six-cysteine peptide SCIFF / SCIFF radical SAM maturase / Anaerobic sulphatase maturase, radical SAM / MoaA/NifB/PqqE, iron-sulphur binding, conserved site / moaA / nifB / pqqE family signature. / 4Fe4S-binding SPASM domain / Iron-sulfur cluster-binding domain / 4Fe-4S single cluster domain / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Radical SAM domain protein / Uncharacterized protein
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.036 Å
AuthorsGrove, T.L. / Himes, P. / Bowers, A. / Bonanno, J.B. / Almo, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
Price Family Foundation United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01 GM118303 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides.
Authors: Grove, T.L. / Himes, P.M. / Hwang, S. / Yumerefendi, H. / Bonanno, J.B. / Kuhlman, B. / Almo, S.C. / Bowers, A.A.
History
DepositionJul 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Radical SAM domain protein
B: CteA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0968
Polymers54,5632
Non-polymers1,5346
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-90 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.917, 153.766, 51.822
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Radical SAM domain protein


Mass: 52285.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)
Strain: ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: Cthe_0906 / Plasmid: pMCSG-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3DDW1
#2: Protein/peptide CteA


Mass: 2277.794 Da / Num. of mol.: 1 / Fragment: UNP residues 1-21 / Source method: obtained synthetically / Details: in-house
Source: (synth.) Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)
References: UniProt: A3DDW2

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Non-polymers , 4 types, 142 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris-HCl 0.2M calcium acetate, 20% polyethylene glycol 3,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 35412 / % possible obs: 98.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.035 / Rrim(I) all: 0.076 / Χ2: 0.836 / Net I/σ(I): 11.3 / Num. measured all: 158323
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.093.90.498172517250.820.2790.5740.64598.1
2.09-2.123.70.48216940.840.2760.5590.68797
2.12-2.163.30.34217320.8950.210.4040.69196.4
2.16-2.213.70.31216970.9270.1790.3620.67598.3
2.21-2.264.60.26917880.9480.1390.3050.75499.8
2.26-2.314.70.22717490.9650.1150.2550.7799.4
2.31-2.374.70.20317760.970.1030.2290.77299.7
2.37-2.434.70.17217270.9780.0870.1940.7999.7
2.43-2.54.70.15317630.980.0780.1730.8499.5
2.5-2.584.70.13417900.9860.0680.150.86999.7
2.58-2.674.70.1217590.9860.0610.1350.89999.6
2.67-2.784.70.117830.990.0510.1120.96399.7
2.78-2.914.70.09117740.9920.0460.1020.92999.5
2.91-3.064.80.0817780.9930.040.090.89599.6
3.06-3.254.70.06917820.9930.0350.0770.92599.7
3.25-3.54.70.06517820.9930.0330.0730.94899.1
3.5-3.864.20.05617620.9950.0310.0640.92297
3.86-4.413.90.0517580.9950.0270.0570.83596.1
4.41-5.555.10.05318220.9950.0260.0590.82798.6
5.55-304.90.05519710.9960.0270.0620.87999.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.036→28.694 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 1771 5.01 %
Rwork0.189 33583 -
obs0.1908 35354 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.73 Å2 / Biso mean: 57.9024 Å2 / Biso min: 21.59 Å2
Refinement stepCycle: final / Resolution: 2.036→28.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 53 136 3747
Biso mean--43.91 51.36 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013734
X-RAY DIFFRACTIONf_angle_d1.5095067
X-RAY DIFFRACTIONf_chiral_restr0.057534
X-RAY DIFFRACTIONf_plane_restr0.006654
X-RAY DIFFRACTIONf_dihedral_angle_d19.2332202
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0365-2.09150.3471220.27572243236586
2.0915-2.15310.34781350.25722534266997
2.1531-2.22250.27841460.23782528267498
2.2225-2.30190.2621330.221825752708100
2.3019-2.39410.25751400.221525952735100
2.3941-2.50290.25651210.215726092730100
2.5029-2.63480.2521350.217426132748100
2.6348-2.79980.28271400.214226022742100
2.7998-3.01570.25451550.21826082763100
3.0157-3.31880.2721330.206826472780100
3.3188-3.79810.23551300.18112605273598
3.7981-4.78160.16691280.15112624275296
4.7816-28.69690.17211530.16112800295399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.63281.7961.23691.79010.47832.33650.1018-0.1116-0.58160.22460.0335-0.42-0.28420.055-0.15840.2586-0.0129-0.01010.34410.02420.4541-7.386511.4229-10.7929
23.49910.94381.07142.946-0.36253.6127-0.22550.37250.35240.05930.1858-0.0604-0.99180.05750.02210.4866-0.04840.02570.35410.03040.263-5.41128.1505-19.2755
33.4660.56031.71961.63-0.53184.552-0.0334-0.5468-0.05690.52130.124-0.0352-0.7027-0.4353-0.0960.40810.03160.03190.34450.00920.2591-7.920418.3048-2.0775
47.0921.49463.31490.9403-0.40833.5060.25360.6475-2.2053-0.21260.883-0.98610.4910.6866-1.08240.44440.00110.08920.4995-0.08710.8353-13.3736-0.5353-24.6266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 177 )A1 - 177
2X-RAY DIFFRACTION2chain 'A' and (resid 178 through 345 )A178 - 345
3X-RAY DIFFRACTION3chain 'A' and (resid 346 through 450 )A346 - 450
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 21 )B1 - 21

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