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- PDB-1p8k: The structure and DNA recognition of a bifunctional homing endonu... -

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Basic information

Entry
Database: PDB / ID: 1p8k
TitleThe structure and DNA recognition of a bifunctional homing endonuclease and group I intron splicing factor
Components
  • 5'-D(P*CP*CP*TP*CP*CP*TP*CP*AP*GP*CP*GP*CP*GP*CP*T)-3'
  • 5'-D(P*GP*CP*GP*CP*GP*CP*TP*GP*AP*GP*GP*AP*GP*GP*TP*TP*TP*C)-3'
  • 5'-D(P*GP*CP*GP*CP*TP*TP*TP*AP*CP*AP*GP*AP*GP*AP*AP*A)-3'
  • 5'-D(P*TP*CP*TP*GP*TP*AP*AP*AP*GP*CP*GP*CP*A)-3'
  • Intron-encoded endonuclease I-AniI
KeywordsHYDROLASE/DNA / HYDROLASE-DNA complex
Function / homology
Function and homology information


intron homing / RNA splicing / mRNA processing / endonuclease activity / Hydrolases; Acting on ester bonds / mitochondrion
Similarity search - Function
LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / : / Cytochrome b/b6/petB / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. ...LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / : / Cytochrome b/b6/petB / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Roll / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Intron-encoded DNA endonuclease I-AniI
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsStoddard, B.L. / Bolduc, J.M.
CitationJournal: Genes Dev. / Year: 2003
Title: Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor.
Authors: Bolduc, J.M. / Spiegel, P.C. / Chatterjee, P. / Brady, K.L. / Downing, M.E. / Caprara, M.G. / Waring, R.B. / Stoddard, B.L.
History
DepositionMay 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE The author claims that Arg61 is correct.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(P*GP*CP*GP*CP*GP*CP*TP*GP*AP*GP*GP*AP*GP*GP*TP*TP*TP*C)-3'
B: 5'-D(P*TP*CP*TP*GP*TP*AP*AP*AP*GP*CP*GP*CP*A)-3'
C: 5'-D(P*GP*CP*GP*CP*TP*TP*TP*AP*CP*AP*GP*AP*GP*AP*AP*A)-3'
D: 5'-D(P*CP*CP*TP*CP*CP*TP*CP*AP*GP*CP*GP*CP*GP*CP*T)-3'
Z: Intron-encoded endonuclease I-AniI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6417
Polymers48,5925
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.462, 72.841, 65.231
Angle α, β, γ (deg.)90.00, 108.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 4 types, 4 molecules ABCD

#1: DNA chain 5'-D(P*GP*CP*GP*CP*GP*CP*TP*GP*AP*GP*GP*AP*GP*GP*TP*TP*TP*C)-3'


Mass: 5588.601 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*TP*CP*TP*GP*TP*AP*AP*AP*GP*CP*GP*CP*A)-3'


Mass: 3975.611 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*GP*CP*GP*CP*TP*TP*TP*AP*CP*AP*GP*AP*GP*AP*AP*A)-3'


Mass: 4931.230 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain 5'-D(P*CP*CP*TP*CP*CP*TP*CP*AP*GP*CP*GP*CP*GP*CP*T)-3'


Mass: 4481.899 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein / Non-polymers , 2 types, 3 molecules Z

#5: Protein Intron-encoded endonuclease I-AniI / mRNA maturase BI1 / COB intron protein


Mass: 29615.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Gene: Aspergillus nidulans / Production host: Escherichia coli (E. coli)
References: UniProt: P03880, Hydrolases; Acting on ester bonds
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG3350, KCl, MgCl2, sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG3350,11
2KCl11
3MgCl211
4sodium citrate11
5KCl12
6MgCl212
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlprotein1drop
2100 mM1reservoirKCl
320 mM1reservoirMgCl2
450 mMsodium citrate1reservoirpH5.0
516-22 %PEG33501reservoir
61

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 2002
RadiationMonochromator: double crystal Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 40.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 9.5
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.21 / % possible all: 61.8
Reflection
*PLUS
Num. obs: 16749 / Redundancy: 12.7 % / Num. measured all: 58621 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 66.2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.264 2630 random
Rwork0.239 --
all0.247 29474 -
obs0.247 27760 -
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 1275 2 0 3362
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.03
RfactorNum. reflection% reflection
Rfree0.48 302 -
Rwork0.45 --
obs--61.8 %
Refinement
*PLUS
Rfactor Rfree: 0.262 / Rfactor Rwork: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.014
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.933

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