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- PDB-1mi8: 2.0 Angstrom crystal structure of a DnaB intein from Synechocysti... -

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Basic information

Entry
Database: PDB / ID: 1mi8
Title2.0 Angstrom crystal structure of a DnaB intein from Synechocystis sp. PCC 6803
ComponentsDnaB intein
KeywordsHYDROLASE / all beta-strands
Function / homology
Function and homology information


primosome complex / intein-mediated protein splicing / DNA 5'-3' helicase / DNA replication, synthesis of primer / DNA helicase activity / endonuclease activity / Hydrolases; Acting on ester bonds / DNA replication / ATP hydrolysis activity / DNA binding ...primosome complex / intein-mediated protein splicing / DNA 5'-3' helicase / DNA replication, synthesis of primer / DNA helicase activity / endonuclease activity / Hydrolases; Acting on ester bonds / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding / cytosol
Similarity search - Function
Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / LAGLIDADG-like domain / DnaB-like helicase C terminal domain / Intein splicing domain ...Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / LAGLIDADG-like domain / DnaB-like helicase C terminal domain / Intein splicing domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Homing endonuclease / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Replicative DNA helicase DnaB
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDing, Y. / Chen, X. / Ferrandon, S. / Xu, M. / Rao, Z.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of mini-intein reveals a conserved catalytic module involved in side chain cyclization of asparagine during protein splicing
Authors: Ding, Y. / Xu, M.Q. / Ghosh, I. / Chen, X. / Ferrandon, S. / Lesage, G. / Rao, Z.
History
DepositionAug 22, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DnaB intein


Theoretical massNumber of molelcules
Total (without water)17,6001
Polymers17,6001
Non-polymers00
Water90150
1
A: DnaB intein

A: DnaB intein


Theoretical massNumber of molelcules
Total (without water)35,2002
Polymers35,2002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)58.17, 58.17, 70.28
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit

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Components

#1: Protein DnaB intein / Replicative DNA helicase


Mass: 17600.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TETHERED DIMER LINKED BY LESSSLQLSPEIEKLSQ / Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Plasmid: pTWIN / Production host: Escherichia coli (E. coli)
References: UniProt: Q55418, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.95 Å3/Da / Density % sol: 36.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG4000, Tris-HCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8 / PH range high: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris1reservoirpH7.5-8.0
216-20 %PEG40001reservoir
34 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 8, 2002
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9307 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2→2.07 Å / % possible all: 75.5
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 97.6 % / Num. measured all: 107903 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 75.5 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 7.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.263 919 RANDOM
Rwork0.21 --
all0.237 9677 -
obs0.226 8794 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1107 0 0 50 1157
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_d2.04
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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