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- PDB-4gig: crystal structure of T69A mutant of trapped Dnae intein precursor -

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Basic information

Entry
Database: PDB / ID: 4gig
Titlecrystal structure of T69A mutant of trapped Dnae intein precursor
ComponentsDNA polymerase III subunit alphaDNA polymerase III holoenzyme
KeywordsSPLICING / intein fold
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 / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) 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 / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) 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 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
DNA polymerase III subunit alpha
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVan Roey, P.
CitationJournal: Protein Sci. / Year: 2013
Title: A conserved threonine spring-loads precursor for intein splicing.
Authors: Dearden, A.K. / Callahan, B. / Roey, P.V. / Li, Z. / Kumar, U. / Belfort, M. / Nayak, S.K.
History
DepositionAug 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8682
Polymers18,7721
Non-polymers961
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.630, 93.630, 41.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

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Components

#1: Protein DNA polymerase III subunit alpha / DNA polymerase III holoenzyme / Ssp dnaE intein


Mass: 18772.209 Da / Num. of mol.: 1 / Fragment: unp residues 775-933 / Mutation: T69A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / Gene: dnaE-N, slr0603, dnaE-C, sll1572 / Production host: Escherichia coli (E. coli) / Strain (production host): origami DE3 / References: UniProt: P74750, DNA-directed DNA polymerase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsK-9 TO G-1 DESIGNATES AN ARTIFICIALLY ENGINEERED N-TERMINAL EXTEIN THAT FORMS A DISULFIDE BOND (CYS- ...K-9 TO G-1 DESIGNATES AN ARTIFICIALLY ENGINEERED N-TERMINAL EXTEIN THAT FORMS A DISULFIDE BOND (CYS-3 TO CYS1) THEREBY INHIBITING THE N-TERMINAL CLEAVING STEP OF THE PROTEIN SPLICING

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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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 52% ammonium sulfate, 100 mM HEPES, 2% isopropanol , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 23, 2012 / Details: Osmics mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→29.61 Å / Num. all: 16781 / Num. obs: 16661 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 2.56 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 13.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.37 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2.5 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
CNS1.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NZM

3nzm


Resolution: 1.8→29.38 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1363247.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1679 10.1 %RANDOM
Rwork0.226 ---
obs0.226 16636 99.2 %-
all-16661 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.3044 Å2 / ksol: 0.361206 e/Å3
Displacement parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å20 Å20 Å2
2--2.73 Å20 Å2
3----5.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 5 112 1391
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.12.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.387 195 9.6 %
Rwork0.341 1844 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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