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- PDB-1zd7: 1.7 Angstrom Crystal Structure Of Post-Splicing Form of a dnaE In... -

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Basic information

Entry
Database: PDB / ID: 1zd7
Title1.7 Angstrom Crystal Structure Of Post-Splicing Form of a dnaE Intein from Synechocystis Sp. Pcc 6803
ComponentsDNA polymerase III alpha subunit
KeywordsTRANSFERASE / DnaE / Intein / Splicing
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 / 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
DNA polymerase III subunit alpha
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSun, P. / Ye, S. / Ferrandon, S. / Evans, T.C. / Xu, M.Q. / Rao, Z.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of an intein from the split dnaE gene of Synechocystis sp. PCC6803 reveal the catalytic model without the penultimate histidine and the mechanism of zinc ion inhibition of protein splicing
Authors: Sun, P. / Ye, S. / Ferrandon, S. / Evans, T.C. / Xu, M.Q. / Rao, Z.
History
DepositionApr 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase III alpha subunit
B: DNA polymerase III alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2226
Polymers35,8382
Non-polymers3844
Water4,324240
1
A: DNA polymerase III alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2074
Polymers17,9191
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA polymerase III alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0152
Polymers17,9191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.247, 67.035, 90.336
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 / DnaE intein


Mass: 17919.068 Da / Num. of mol.: 2 / Fragment: residues 1-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Plasmid: pMYB5 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P74750, DNA-directed DNA polymerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium Sulfate, PEG 400, Sodium Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.97916 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 13, 2004
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 35427 / Num. obs: 35350 / % possible obs: 98.11 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.7→1.73 Å / % possible all: 81.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2018 943 random
Rwork0.1766 --
all0.1825 35427 -
obs0.179 35350 -
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 20 240 2778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.9248
X-RAY DIFFRACTIONc_bond_d0.0197
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d1.56

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