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- PDB-5ol7: Crystal structure of an inactivated Npu SICLOPPS intein with CFAH... -

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Basic information

Entry
Database: PDB / ID: 5ol7
TitleCrystal structure of an inactivated Npu SICLOPPS intein with CFAHPQ extein
ComponentsDNA-directed DNA polymerase,DNA-directed DNA polymerase
KeywordsSPLICING / intein / extein / SICLOPPS / cyclic peptide
Function / homology
Function and homology information


intein-mediated protein splicing / 3'-5' exonuclease activity / helicase activity / DNA replication / nucleic acid binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / metal ion binding
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 / Hint domain superfamily / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain
Similarity search - Domain/homology
: / DNA polymerase III, alpha subunit / Nucleic acid binding, OB-fold, tRNA/helicase-type
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsKick, L.M. / Schneider, S.
Funding support Germany, 4items
OrganizationGrant numberCountry
Center for Integrated Protein Science Germany
German Research FoundationSCHN1273 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 1.2May 8, 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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Assembly

Deposited unit
A: DNA-directed DNA polymerase,DNA-directed DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5063
Polymers17,4071
Non-polymers992
Water2,558142
1
A: DNA-directed DNA polymerase,DNA-directed DNA polymerase
hetero molecules

A: DNA-directed DNA polymerase,DNA-directed DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0116
Polymers34,8132
Non-polymers1984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_875-x+3,-y+2,z1
Buried area1420 Å2
ΔGint-46 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.920, 68.417, 95.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-202-

CO

21A-317-

HOH

31A-340-

HOH

41A-400-

HOH

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Components

#1: Protein DNA-directed DNA polymerase,DNA-directed DNA polymerase


Mass: 17406.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (strain ATCC 29133 / PCC 73102) (bacteria)
Gene: Npun_F4872 / Plasmid: pBAD / Strain: ATCC 29133 / PCC 73102 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B2J821, UniProt: B2J066, DNA-directed DNA polymerase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200mM calcium acetate, 100mM MES pH 6.5, 10% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→32.7 Å / Num. obs: 24628 / % possible obs: 94.7 % / Redundancy: 5.1 % / CC1/2: 0.999 / Net I/σ(I): 18
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2517 / CC1/2: 0.842 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementResolution: 1.6→32.679 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.78 / Phase error: 20.32
RfactorNum. reflection% reflection
Rfree0.1898 2325 5.01 %
Rwork0.1565 --
obs0.1581 46410 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→32.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 2 142 1299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061202
X-RAY DIFFRACTIONf_angle_d0.9671630
X-RAY DIFFRACTIONf_dihedral_angle_d2.9641006
X-RAY DIFFRACTIONf_chiral_restr0.057179
X-RAY DIFFRACTIONf_plane_restr0.005214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.63270.37811420.38572668X-RAY DIFFRACTION97
1.6327-1.66820.46471420.33342672X-RAY DIFFRACTION97
1.6682-1.7070.26681390.28462683X-RAY DIFFRACTION97
1.707-1.74970.26281400.24462662X-RAY DIFFRACTION97
1.7497-1.7970.26461400.1992673X-RAY DIFFRACTION96
1.797-1.84980.20121330.16972594X-RAY DIFFRACTION94
1.8498-1.90950.18781360.15622658X-RAY DIFFRACTION96
1.9095-1.97780.20141370.16052639X-RAY DIFFRACTION96
1.9778-2.0570.15711440.13922656X-RAY DIFFRACTION95
2.057-2.15060.18841390.12932555X-RAY DIFFRACTION94
2.1506-2.26390.17571440.12642628X-RAY DIFFRACTION94
2.2639-2.40570.18211330.13572543X-RAY DIFFRACTION93
2.4057-2.59140.15061340.14512527X-RAY DIFFRACTION92
2.5914-2.8520.17071330.14932555X-RAY DIFFRACTION92
2.852-3.26440.21751260.14812517X-RAY DIFFRACTION91
3.2644-4.11150.18081340.14082483X-RAY DIFFRACTION90
4.1115-32.68580.16171290.15412372X-RAY DIFFRACTION86

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