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- PDB-5ol1: Crystal structure of an inactivated Ssp SICLOPPS intein with a CA... -

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Basic information

Entry
Database: PDB / ID: 5ol1
TitleCrystal structure of an inactivated Ssp SICLOPPS intein with a CAFHPQ extein
ComponentsDNA polymerase III subunit alpha,DNA polymerase III subunit alphaDNA polymerase III holoenzyme
KeywordsSPLICING / intein / extein / SICLOPPS / cyclic peptide
Function / homology
Function and homology information


intein-mediated protein splicing / 3'-5' exonuclease activity / DNA replication / nucleic acid binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / cytoplasm
Similarity search - Function
Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / PHP domain / PHP domain ...Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / Hint domain superfamily / OB-fold nucleic acid binding domain
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / TRIETHYLENE GLYCOL / DNA polymerase III subunit alpha
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 Å
AuthorsKick, L.M. / Schneider, S.
Funding support Germany, 4items
OrganizationGrant numberCountry
Center for Integrated Protein Science Germany
German Research FoundationSCHN 1273 Germany
German Research FoundationSFB749 Germany
Fonds der chemischen Industrie Germany
CitationJournal: Chembiochem / Year: 2017
Title: Mechanistic Insights into Cyclic Peptide Generation by DnaE Split-Inteins through Quantitative and Structural Investigation.
Authors: Kick, L.M. / Harteis, S. / Koch, M.F. / Schneider, S.
History
DepositionJul 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: 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_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III subunit alpha,DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9346
Polymers18,4521
Non-polymers4835
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-26 kcal/mol
Surface area6740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.233, 43.304, 96.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase III subunit alpha,DNA polymerase III subunit alpha / DNA polymerase III holoenzyme


Mass: 18451.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Act
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Gene: dnaE-N, slr0603, dnaE-C, sll1572 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P74750, DNA-directed DNA polymerase

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Non-polymers , 5 types, 122 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100mM MES pH 6.5, 2M (NH4)2SO4, 5%(w/v) PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.75→48.1 Å / Num. obs: 17540 / % possible obs: 99.8 % / Redundancy: 5.4 % / CC1/2: 0.94 / Net I/σ(I): 3.6
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 5.4 % / Num. unique obs: 1694 / CC1/2: 0.409 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
PHASER2.6.1phasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GIG

4gig


Resolution: 1.751→48.066 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.38
RfactorNum. reflection% reflection
Rfree0.2313 1632 5.01 %
Rwork0.1978 --
obs0.1994 32548 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.751→48.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 0 28 117 1245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051182
X-RAY DIFFRACTIONf_angle_d0.8131601
X-RAY DIFFRACTIONf_dihedral_angle_d12.524955
X-RAY DIFFRACTIONf_chiral_restr0.052180
X-RAY DIFFRACTIONf_plane_restr0.005207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7514-1.8030.29941370.3022543X-RAY DIFFRACTION98
1.803-1.86120.34571340.27742551X-RAY DIFFRACTION100
1.8612-1.92770.30181350.26952582X-RAY DIFFRACTION100
1.9277-2.00490.26631380.24372605X-RAY DIFFRACTION100
2.0049-2.09610.27291330.22612551X-RAY DIFFRACTION100
2.0961-2.20660.22731380.20792593X-RAY DIFFRACTION100
2.2066-2.34490.21821370.19982606X-RAY DIFFRACTION100
2.3449-2.52590.25321380.19322570X-RAY DIFFRACTION100
2.5259-2.78010.24231360.19712566X-RAY DIFFRACTION100
2.7801-3.18230.22181330.17892569X-RAY DIFFRACTION100
3.1823-4.0090.1961360.17282611X-RAY DIFFRACTION100
4.009-48.08360.20671370.17312569X-RAY DIFFRACTION100
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)
15.08090.3038-0.96854.9188-1.06237.4745-0.05380.19180.3927-0.03180.14950.4113-0.7043-0.0916-0.15520.23480.01-0.04240.1057-0.03170.2302-3.59650.98818.2342
27.459-0.0445-2.58413.05350.0914.85040.0994-0.0691-0.13330.0459-0.1149-0.00040.1356-0.07220.03530.121-0.0306-0.03890.1556-0.00730.0998-4.6613-13.73347.783
37.51351.5891-1.17577.4777-0.50263.83730.31090.34980.08020.01410.011-0.2785-0.06390.1296-0.27790.08680.03460.00290.2657-0.01110.1402-2.3607-10.56380.7054
44.94890.0983-4.58121.33050.63344.77670.2401-0.4279-0.1655-0.1405-0.29830.35270.3860.57620.10950.2245-0.0412-0.07710.26680.01240.21380.7351-18.10843.0355
52.59020.82180.70722.57491.51793.2678-0.02260.04730.0260.10350.0210.0020.0066-0.25940.00250.13890.0002-0.01440.14260.0170.1596-5.1077-8.278317.6878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 67 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 122 )
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 9 )
5X-RAY DIFFRACTION5chain 'A' and (resid 10 through 66 )

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