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- PDB-7oec: Crystal structure of an intein from a hyperthermophile -

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Basic information

Entry
Database: PDB / ID: 7oec
TitleCrystal structure of an intein from a hyperthermophile
ComponentsDNA polymerase II large subunit
KeywordsSPLICING / protein splicing / intein
Function / homology
Function and homology information


exodeoxyribonuclease I / intein-mediated protein splicing / single-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / identical protein binding
Similarity search - Function
DNA polymerase II large subunit DP2 / DNA polymerase II large subunit DP2, N-terminal / : / : / DNA polymerase II large subunit DP2, N-terminal / DNA polymerase II large subunit DP2, central domain / DNA polymerase II large subunit DP2, catalytic domain / Intein splicing domain / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. ...DNA polymerase II large subunit DP2 / DNA polymerase II large subunit DP2, N-terminal / : / : / DNA polymerase II large subunit DP2, N-terminal / DNA polymerase II large subunit DP2, central domain / DNA polymerase II large subunit DP2, catalytic domain / Intein splicing domain / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / 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 / HNH nuclease
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / DNA polymerase II large subunit
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsHannes, B. / Hiltunen, M. / Iwai, H.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland137995, 277335, 336450 Finland
Citation
Journal: Microorganisms / Year: 2021
Title: Mini-Intein Structures from Extremophiles Suggest a Strategy for Finding Novel Robust Inteins.
Authors: Hiltunen, M.K. / Beyer, H.M. / Iwai, H.
#1: Journal: Preprints / Year: 2021
Title: Mini-Intein Structures from Extremophiles Suggest a Strategy for Finding Novel Robust Inteins
Authors: Hiltunen, M.K. / Beyer, H.M. / Iwai, H.
History
DepositionMay 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase II large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9897
Polymers19,4541
Non-polymers5356
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-46 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.820, 70.820, 70.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

21A-368-

HOH

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Components

#1: Protein DNA polymerase II large subunit / Pol II / Exodeoxyribonuclease large subunit


Mass: 19454.188 Da / Num. of mol.: 1 / Mutation: C1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: polC, PH0121 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express
References: UniProt: O57861, DNA-directed DNA polymerase, exodeoxyribonuclease I
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES pH 6, 15 % (W/v) PEG 550 MME, 30 mM zinc sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 24, 2019
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.48→35.41 Å / Num. obs: 30560 / % possible obs: 99.87 % / Redundancy: 25.4 % / Biso Wilson estimate: 23.39 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.35
Reflection shellResolution: 1.48→1.533 Å / Mean I/σ(I) obs: 4.22 / Num. unique obs: 2977 / CC1/2: 0.445 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PDB_EXTRACT1.18.2_3874data extraction
PHENIX1.18.2_3874refinement
GDAdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RPQ

6rpq


Resolution: 1.48→35.41 Å / SU ML: 0.1201 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.5066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1868 2864 5.01 %
Rwork0.1538 54339 -
obs0.1555 30534 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.71 Å2
Refinement stepCycle: LAST / Resolution: 1.48→35.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1362 0 26 76 1464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01691444
X-RAY DIFFRACTIONf_angle_d1.48291959
X-RAY DIFFRACTIONf_chiral_restr0.1125222
X-RAY DIFFRACTIONf_plane_restr0.0092251
X-RAY DIFFRACTIONf_dihedral_angle_d19.1743550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.510.27341420.19472719X-RAY DIFFRACTION99.41
1.51-1.530.27651400.17992691X-RAY DIFFRACTION99.89
1.53-1.560.20391490.15392728X-RAY DIFFRACTION99.97
1.56-1.590.20411410.14962711X-RAY DIFFRACTION100
1.59-1.630.17911430.13692690X-RAY DIFFRACTION100
1.63-1.670.1831450.12592765X-RAY DIFFRACTION100
1.67-1.710.19471420.12192678X-RAY DIFFRACTION100
1.71-1.750.17271490.12062750X-RAY DIFFRACTION100
1.75-1.810.21521430.11672728X-RAY DIFFRACTION100
1.81-1.860.17891470.12792734X-RAY DIFFRACTION100
1.86-1.930.18251430.11592697X-RAY DIFFRACTION100
1.93-2.010.16891420.12582706X-RAY DIFFRACTION100
2.01-2.10.19591390.12362716X-RAY DIFFRACTION100
2.1-2.210.16211390.12812735X-RAY DIFFRACTION100
2.21-2.350.20841410.12812726X-RAY DIFFRACTION100
2.35-2.530.17111470.14242702X-RAY DIFFRACTION100
2.53-2.780.15621390.17182739X-RAY DIFFRACTION100
2.78-3.190.22641440.18222713X-RAY DIFFRACTION100
3.19-4.010.17931450.17092720X-RAY DIFFRACTION99.97
4.02-35.410.18391440.16292691X-RAY DIFFRACTION98.61

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