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- PDB-4kl5: Crystal structure of NpuDnaE intein -

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Basic information

Entry
Database: PDB / ID: 4kl5
TitleCrystal structure of NpuDnaE intein
ComponentsDNA polymerase III, alpha subunit, Nucleic acid binding, OB-fold, tRNA/helicase-type chimeric construct
KeywordsUNKNOWN FUNCTION / HINT / intein / NpuDnaE inten
Function / homology
Function and homology information


intein-mediated protein splicing / 3'-5' exonuclease activity / helicase activity / DNA-directed DNA polymerase / nucleic acid binding / DNA-directed DNA polymerase activity / DNA replication / 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 / 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 / Hint domain superfamily / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / 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: 1.72 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 1.2Jun 11, 2014Group: Derived calculations
Revision 1.3Aug 9, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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, alpha subunit, Nucleic acid binding, OB-fold, tRNA/helicase-type chimeric construct
B: DNA polymerase III, alpha subunit, Nucleic acid binding, OB-fold, tRNA/helicase-type chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2315
Polymers32,7552
Non-polymers4763
Water3,981221
1
A: DNA polymerase III, alpha subunit, Nucleic acid binding, OB-fold, tRNA/helicase-type chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7623
Polymers16,3771
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase III, alpha subunit, Nucleic acid binding, OB-fold, tRNA/helicase-type chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4692
Polymers16,3771
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: DNA polymerase III, alpha subunit, Nucleic acid binding, OB-fold, tRNA/helicase-type chimeric construct
hetero molecules

B: DNA polymerase III, alpha subunit, Nucleic acid binding, OB-fold, tRNA/helicase-type chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2315
Polymers32,7552
Non-polymers4763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area2090 Å2
ΔGint-5 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.555, 66.700, 67.486
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA polymerase III, alpha subunit, Nucleic acid binding, OB-fold, tRNA/helicase-type chimeric construct


Mass: 16377.375 Da / Num. of mol.: 2
Fragment: NpuDnaE Intein (unp residues 775-876, unp residues 2-40)
Mutation: C1A, D142N, D143S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: ATCC 29133 / PCC 73102 / Gene: DnaE N- and C-intein part, Npun_F4872 / Plasmid: pALBRSF12 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: B2J066, UniProt: B2J821, DNA-directed DNA polymerase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.98 Å3/Da / Density % sol: 37.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.4 M tri-ammonium citrate/citric acid , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2011
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. all: 28489 / Num. obs: 28252 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.04 % / Rmerge(I) obs: 0.065
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.72-1.827.10.5483.674373196.3
1.82-1.947.30.3026.724244199.9
1.94-2.17.30.16911.6939981100
2.1-2.37.20.11217.5536721100
2.3-2.577.20.08122.633461100
2.57-2.9770.05531.6429631100
2.97-3.636.60.03843.925321100
3.63-5.126.70.02753.251997199.7
5.12-506.20.02750.681127195.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2KEQ

2keq


Resolution: 1.72→47.439 Å / SU ML: 0.16 / σ(F): 3.67 / σ(I): 3.67 / Phase error: 19.97 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 1413 5 %RANDOM
Rwork0.1693 ---
obs0.1712 28251 99.16 %-
all-28489 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→47.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 32 221 2499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012391
X-RAY DIFFRACTIONf_angle_d1.2513248
X-RAY DIFFRACTIONf_dihedral_angle_d17.748914
X-RAY DIFFRACTIONf_chiral_restr0.098354
X-RAY DIFFRACTIONf_plane_restr0.005431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7153-1.77660.27631320.22312499X-RAY DIFFRACTION94
1.7766-1.84770.261400.20042671X-RAY DIFFRACTION100
1.8477-1.93180.25531400.19082665X-RAY DIFFRACTION100
1.9318-2.03370.21711400.18352659X-RAY DIFFRACTION100
2.0337-2.16110.24721420.16372692X-RAY DIFFRACTION100
2.1611-2.32790.19221410.17052686X-RAY DIFFRACTION100
2.3279-2.56220.23071420.17722685X-RAY DIFFRACTION100
2.5622-2.93290.23991430.18362725X-RAY DIFFRACTION100
2.9329-3.69490.2011450.15882743X-RAY DIFFRACTION100
3.6949-47.45760.16081480.15042813X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 1.4747 Å / Origin y: 1.2687 Å / Origin z: 8.8625 Å
111213212223313233
T0.1179 Å20.0238 Å20.0324 Å2-0.0964 Å2-0.0029 Å2--0.0746 Å2
L1.3636 °20.7096 °20.1672 °2-1.4087 °2-0.0237 °2--0.7683 °2
S-0.066 Å °0.0409 Å °0.0427 Å °-0.0236 Å °0.0919 Å °0.0717 Å °-0.0103 Å °-0.0164 Å °-0.027 Å °
Refinement TLS groupSelection details: all

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