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Basic information

Entry
Database: PDB / ID: 5why
TitleStructural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides
ComponentsRadical 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
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. ...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
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.692 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 18, 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 1.4Oct 4, 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 / 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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_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: Radical SAM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,67715
Polymers104,5702
Non-polymers3,10713
Water1086
1
A: Radical SAM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7796
Polymers52,2851
Non-polymers1,4935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Radical SAM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8999
Polymers52,2851
Non-polymers1,6148
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.929, 59.357, 81.363
Angle α, β, γ (deg.)83.090, 73.310, 66.630
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Radical SAM domain protein


Mass: 52285.082 Da / Num. of mol.: 2
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: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 41.67 % / Mosaicity: 0.632 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.2M calcium chloride, 25% polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0333 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 2.692→30 Å / Num. obs: 23072 / % possible obs: 98 % / Redundancy: 1.8 % / Biso Wilson estimate: 66.75 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.06 / Rrim(I) all: 0.085 / Χ2: 0.709 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.751.70.46811190.6920.4680.6620.4296.5
2.75-2.81.80.4140.7170.4140.5850.41797.7
2.8-2.851.80.360.8950.360.510.48497.3
2.85-2.911.80.3120.8220.3120.4410.4697.1
2.91-2.971.80.2530.8670.2530.3580.4497.1
2.97-3.041.80.230.8220.230.3260.52598
3.04-3.121.80.1720.9340.1720.2440.50597.4
3.12-3.21.80.1450.9540.1450.2040.55597.5
3.2-3.291.70.1240.9570.1240.1750.57498.3
3.29-3.41.80.1060.9660.1060.150.57397.3
3.4-3.521.70.090.9790.090.1270.66598.4
3.52-3.661.70.0730.9820.0730.1030.67598.6
3.66-3.831.80.0620.9860.0620.0870.68998.7
3.83-4.031.80.0510.9920.0510.0720.6198.6
4.03-4.281.80.0470.9910.0470.0660.73798.6
4.28-4.611.70.0440.9910.0440.0620.79698.5
4.61-5.071.70.0440.9910.0440.0620.91198.5
5.07-5.81.80.0450.9910.0450.0630.92999.2
5.8-7.31.80.0480.9890.0480.0671.17797.9
7.3-301.80.0460.9910.0460.0662.01199.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WGG

5wgg


Resolution: 2.692→29.684 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 35.32
RfactorNum. reflection% reflection
Rfree0.2812 1974 8.58 %
Rwork0.2245 --
obs0.2296 23002 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.88 Å2 / Biso mean: 80.2725 Å2 / Biso min: 56.17 Å2
Refinement stepCycle: final / Resolution: 2.692→29.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6572 0 107 6 6685
Biso mean--69.53 71.16 -
Num. residues----839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076833
X-RAY DIFFRACTIONf_angle_d0.959280
X-RAY DIFFRACTIONf_chiral_restr0.058982
X-RAY DIFFRACTIONf_plane_restr0.0041196
X-RAY DIFFRACTIONf_dihedral_angle_d19.5323982
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 (%)
2.6919-2.75920.44461190.37981339145887
2.7592-2.83370.3921420.34191512165497
2.8337-2.9170.38341400.32121508164897
2.917-3.01110.39311370.31691512164997
3.0111-3.11860.3731520.29781488164098
3.1186-3.24330.34731430.27851519166298
3.2433-3.39080.39961280.27381517164597
3.3908-3.56920.3471380.26411499163798
3.5692-3.79240.30971490.23431528167799
3.7924-4.08460.30121460.2231523166999
4.0846-4.49440.23781470.19681515166298
4.4944-5.14180.24591400.18011545168598
5.1418-6.46710.26471450.20811509165499
6.4671-29.68530.18771480.1671514166299
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)
13.4543-1.034-0.24274.13490.06814.39340.1484-0.3796-0.99060.9382-0.1844-0.2341-0.2206-0.07380.13070.64070.02320.05670.81450.37040.9305-29.8308-3.428711.9211
22.69440.478-1.23020.5644-0.57271.5132-0.10210.0996-0.06550.1491-0.0571-0.1079-0.45140.1160.1030.6351-0.0381-0.090.47240.07910.5933-5.69257.8454-26.0622
32.6553-0.62380.16661.8019-0.53753.1727-0.0448-0.14-0.41240.07750.09610.1873-0.0497-0.5168-0.02570.4098-0.0018-0.02070.38750.05080.4476-15.97012.1658-26.4847
46.05013.6121-1.80712.0719-0.77293.88130.361-0.4985-0.97540.6734-0.3314-0.598-0.78820.0214-0.19630.67480.0711-0.00380.56690.15030.6582-14.60848.4016-7.3076
52.36-0.92890.94140.83310.2438.2963-0.42380.44730.3369-0.9979-0.3132-0.22450.86120.03590.40671.1262-0.13140.12770.46570.13410.712-8.3024-24.1711-22.3059
61.40310.35420.33561.5533-0.14463.5902-0.0505-0.10520.31560.3725-0.1986-0.4204-0.8122-0.13130.2380.78550.0105-0.20930.45930.08650.6927-10.0575-19.373124.5556
72.0874-0.51050.44455.8758-0.36594.0657-0.1086-0.06380.05930.13160.0675-0.08390.2505-0.40370.06140.4428-0.0116-0.07850.48460.08610.4563-23.2017-31.191619.9687
81.74160.72620.81722.1872-0.8072.723-0.2598-0.16460.07-0.1038-0.1187-0.4066-0.1839-0.06440.36450.6484-0.0182-0.04560.4440.07690.5825-10.9254-28.546512.1284
91.34480.05220.69983.3772-1.03614.5426-0.2791-0.02470.1998-0.2369-0.4031-1.1217-0.2360.88480.73470.7552-0.10410.01810.68270.19690.8138-1.7945-25.45734.5791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 71 )A1 - 71
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 140 )A72 - 140
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 382 )A141 - 382
4X-RAY DIFFRACTION4chain 'A' and (resid 383 through 448 )A383 - 448
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 70 )B1 - 70
6X-RAY DIFFRACTION6chain 'B' and (resid 71 through 177 )B71 - 177
7X-RAY DIFFRACTION7chain 'B' and (resid 178 through 273 )B178 - 273
8X-RAY DIFFRACTION8chain 'B' and (resid 274 through 382 )B274 - 382
9X-RAY DIFFRACTION9chain 'B' and (resid 383 through 448 )B383 - 448

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