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- PDB-4lx3: Conserved Residues that Modulate Protein trans-Splicing of Npu Dn... -

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Basic information

Entry
Database: PDB / ID: 4lx3
TitleConserved Residues that Modulate Protein trans-Splicing of Npu DnaE Split Intein
Components
  • DNA polymerase III, alpha subunit
  • Nucleic acid binding, OB-fold, tRNA/helicase-type
KeywordsTRANSFERASE / trans-structure / naturally occurring
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 / SAD / Resolution: 1.5 Å
AuthorsWu, Q. / Gao, Z. / Wei, Y. / Ma, G. / Zheng, Y. / Dong, Y. / Liu, Y.
CitationJournal: Biochem.J. / Year: 2014
Title: Conserved residues that modulate protein trans-splicing of Npu DnaE split intein.
Authors: Wu, Q. / Gao, Z. / Wei, Y. / Ma, G. / Zheng, Y. / Dong, Y. / Liu, Y.
History
DepositionJul 29, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_conn / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III, alpha subunit
B: Nucleic acid binding, OB-fold, tRNA/helicase-type


Theoretical massNumber of molelcules
Total (without water)17,0172
Polymers17,0172
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-25 kcal/mol
Surface area6960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.029, 61.199, 103.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-117-

HOH

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Components

#1: Protein DNA polymerase III, alpha subunit /


Mass: 12836.946 Da / Num. of mol.: 1 / Fragment: UNP residues 775-876
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: ATCC 29133 / PCC 73102 / Gene: Npun_F4872 / Production host: Escherichia coli (E. coli) / References: UniProt: B2J066, DNA-directed DNA polymerase
#2: Protein/peptide Nucleic acid binding, OB-fold, tRNA/helicase-type


Mass: 4179.662 Da / Num. of mol.: 1 / Fragment: UNP residues 1-36
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: ATCC 29133 / PCC 73102 / Gene: Npun_F5684 / Production host: Escherichia coli (E. coli) / References: UniProt: B2J821, DNA-directed DNA polymerase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8
Details: 20mM Tris-HCl, 100mM NaCl, 2mM Dithiothreitol, pH 8.0, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 22, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→33.8 Å / Num. all: 22916 / Num. obs: 22916 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.5→1.53 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→33.8 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.19 / σ(F): 1.36 / Phase error: 16.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1943 1174 5.12 %random
Rwork0.1673 ---
all0.1686 22916 --
obs0.1673 22916 99.99 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.471 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 51.41 Å2 / Biso mean: 12.7125 Å2 / Biso min: 3.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.3005 Å20 Å20 Å2
2---0.148 Å2-0 Å2
3----0.1525 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 0 215 1329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011203
X-RAY DIFFRACTIONf_angle_d1.3521625
X-RAY DIFFRACTIONf_dihedral_angle_d14.367472
X-RAY DIFFRACTIONf_chiral_restr0.085178
X-RAY DIFFRACTIONf_plane_restr0.005211
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.56830.27171490.210126962845
1.5683-1.6510.19311340.172126792813
1.651-1.75440.21551510.162626622813
1.7544-1.88990.20171450.153227062851
1.8899-2.080.18851490.158726962845
2.08-2.3810.18391630.159626872850
2.381-2.99950.20711360.16827442880
2.9995-33.80880.17341470.170928723019
Refinement TLS params.Method: refined / Origin x: 13.6415 Å / Origin y: 14.1408 Å / Origin z: 12.5822 Å
111213212223313233
T0.0396 Å20.0048 Å2-0.0016 Å2-0.0515 Å2-0.0013 Å2--0.0383 Å2
L0.6608 °20.1041 °20.2798 °2-0.9001 °2-0.0751 °2--0.6729 °2
S-0.002 Å °0.0629 Å °0.0171 Å °-0.0512 Å °0.0032 Å °0.0371 Å °-0.0136 Å °-0.0244 Å °-0.0042 Å °
Refinement TLS groupSelection details: all

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