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- PDB-4kl6: Crystal structure of dimeric form of NpuDnaE intein -

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Basic information

Entry
Database: PDB / ID: 4kl6
TitleCrystal structure of dimeric form of NpuDnaE intein
ComponentsDNA-directed DNA polymerase,Nucleic acid binding, OB-fold, tRNA/helicase-type
KeywordsUNKNOWN FUNCTION / HINT / intein / domain swapped / NpuDnaE inten
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
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, alpha subunit / Nucleic acid binding, OB-fold, tRNA/helicase-type
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAranko, A.S. / Oeemig, J.S. / Kajander, T. / Iwai, H.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Intermolecular domain swapping induces intein-mediated protein alternative splicing.
Authors: Aranko, A.S. / Oeemig, J.S. / Kajander, T. / Iwai, H.
History
DepositionMay 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2May 31, 2017Group: Structure summary
Revision 1.3Sep 20, 2023Group: 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-directed DNA polymerase,Nucleic acid binding, OB-fold, tRNA/helicase-type
D: DNA-directed DNA polymerase,Nucleic acid binding, OB-fold, tRNA/helicase-type
C: DNA-directed DNA polymerase,Nucleic acid binding, OB-fold, tRNA/helicase-type
B: DNA-directed DNA polymerase,Nucleic acid binding, OB-fold, tRNA/helicase-type


Theoretical massNumber of molelcules
Total (without water)62,4224
Polymers62,4224
Non-polymers00
Water5,080282
1
A: DNA-directed DNA polymerase,Nucleic acid binding, OB-fold, tRNA/helicase-type
B: DNA-directed DNA polymerase,Nucleic acid binding, OB-fold, tRNA/helicase-type


Theoretical massNumber of molelcules
Total (without water)31,2112
Polymers31,2112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-54 kcal/mol
Surface area13110 Å2
MethodPISA
2
D: DNA-directed DNA polymerase,Nucleic acid binding, OB-fold, tRNA/helicase-type
C: DNA-directed DNA polymerase,Nucleic acid binding, OB-fold, tRNA/helicase-type


Theoretical massNumber of molelcules
Total (without water)31,2112
Polymers31,2112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9400 Å2
ΔGint-54 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.720, 64.010, 64.220
Angle α, β, γ (deg.)109.02, 99.53, 95.52
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DNA-directed DNA polymerase,Nucleic acid binding, OB-fold, tRNA/helicase-type


Mass: 15605.601 Da / Num. of mol.: 4
Fragment: NpuDnaE Intein (unp residues 775-876, unp residues 2-37)
Mutation: C775A, C37S,C775A, C37S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: ATCC 29133 / PCC 73102 / Gene: Npun_F4872, Npun_F5684 / Plasmid: pHYRSF236 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: B2J066, UniProt: B2J821, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, 2.0 M ammonium phosphate , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2010 / Details: monochromator crystals
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 29589 / Num. obs: 27269 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.068
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.2-2.331.80.3422.128014190.6
2.33-2.491.80.2463.047834192.7
2.49-2.691.70.1793.917041192.8
2.69-2.951.70.1096.426667193.4
2.95-3.291.70.0689.926057192.7
3.29-3.81.70.04614.645092191.2
3.8-4.641.70.03121.154470191.4
4.64-6.521.60.03219.133331191.4
6.52-501.70.02325.41967194.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2KEQ

2keq


Resolution: 2.2→19.976 Å / SU ML: 0.34 / σ(F): 2 / σ(I): 2 / Phase error: 27.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2656 1361 5 %RANDOM
Rwork0.1965 ---
obs0.2 25872 92.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.144 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9714 Å21.6957 Å2-1.7158 Å2
2--1.6734 Å23.5702 Å2
3----0.702 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4292 0 0 282 4574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014379
X-RAY DIFFRACTIONf_angle_d1.2785922
X-RAY DIFFRACTIONf_dihedral_angle_d14.6651622
X-RAY DIFFRACTIONf_chiral_restr0.088649
X-RAY DIFFRACTIONf_plane_restr0.005777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2003-2.27880.31651300.23912464X-RAY DIFFRACTION89
2.2788-2.36990.29191390.2192648X-RAY DIFFRACTION93
2.3699-2.47760.32681380.20422617X-RAY DIFFRACTION93
2.4776-2.60790.31911350.23762573X-RAY DIFFRACTION93
2.6079-2.77090.35151360.23532590X-RAY DIFFRACTION92
2.7709-2.98420.30481390.21742640X-RAY DIFFRACTION94
2.9842-3.28330.28061380.20122606X-RAY DIFFRACTION93
3.2833-3.75570.25511340.19162551X-RAY DIFFRACTION91
3.7557-4.72150.19111350.14722565X-RAY DIFFRACTION92
4.7215-19.97680.22751370.192614X-RAY DIFFRACTION93

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