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- PDB-1a73: INTRON-ENCODED ENDONUCLEASE I-PPOI COMPLEXED WITH DNA -

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Basic information

Entry
Database: PDB / ID: 1a73
TitleINTRON-ENCODED ENDONUCLEASE I-PPOI COMPLEXED WITH DNA
Components
  • DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3')
  • DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')
  • INTRON 3 (I-PPO) ENCODED ENDONUCLEASE
KeywordsHYDROLASE/DNA / COMPLEX (HOMING ENDONUCLEASE-DNA) / INTRON / ZINC / DNA BINDING / PROTEIN FOLDING / HYDROLASE-DNA COMPLEX
Function / homologyZinc-binding loop region of homing endonuclease / Zinc-binding loop region of homing endonuclease / intron homing / endonuclease activity / Acting on Ester Bonds / Intron-encoded endonuclease I-PpoI
Function and homology information
Specimen sourcePhysarum polycephalum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / 1.8 Å resolution
AuthorsFlick, K.E. / Monnat Junior, R.J. / Stoddard, B.L.
Citation
Journal: Nature / Year: 1998
Title: DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.
Authors: Flick, K.E. / Jurica, M.S. / Monnat Jr., R.J. / Stoddard, B.L.
#1: Journal: Protein Sci. / Year: 1997
Title: Crystallization and Preliminary X-Ray Studies of I-Ppoi: A Nuclear, Intron- Encoded Homing Endonuclease from Physarum Polycephalum
Authors: Flick, K.E. / Mchugh, D. / Heath, J.D. / Stephens, K.M. / Monnat Junior, R.J. / Stoddard, B.L.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 19, 1998 / Release: Oct 14, 1998
RevisionDateData content typeGroupProviderType
1.0Oct 14, 1998Structure modelrepositoryInitial release
1.1May 22, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3')
D: DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')
E: DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3')
F: DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')
A: INTRON 3 (I-PPO) ENCODED ENDONUCLEASE
B: INTRON 3 (I-PPO) ENCODED ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,71712
Polyers48,4076
Non-polymers3106
Water7,044391
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)113.700, 113.700, 88.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP 31 2 1

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Components

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DNA chain , 2 types, 4 molecules CEDF

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


Mass: 3916.571 Da / Num. of mol.: 2 / Fragment: ENDONUCLEASE I-PPOI BINDING SEQUENCE
#2: DNA chain DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')


Mass: 2475.655 Da / Num. of mol.: 2 / Fragment: ENDONUCLEASE I-PPOI BINDING SEQUENCE

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Protein/peptide , 1 types, 2 molecules AB

#3: Protein/peptide INTRON 3 (I-PPO) ENCODED ENDONUCLEASE / INTRON-ENCODED ENDONUCLEASE I-PPOI


Mass: 17811.242 Da / Num. of mol.: 2 / Fragment: ENDONUCLEASE (I-PPO) ENCODED ENDONUCLEASE / Source: (gene. exp.) Physarum polycephalum (eukaryote) / Genus: Physarum / Cellular location: NUCLEUSCell nucleus / Plasmid name: PET / Genus (production host): Escherichia / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q94702

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Non-polymers , 3 types, 397 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Formula: Zn / Zinc
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Formula: H2O / Water

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Details

Compound detailsADENOSINES C 21 AND D 21 ARE SITES OF ENDONUCLEASE CLEAVAGE

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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: 3.4 / Density percent sol: 60 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: THE CRYSTALS WERE GROWN FROM A 2:1 MOLAR RATIO SOLUTION OF PROTEIN AND DNA SUPPLEMENTED WITH 2.5 MM EDTA AND 5 MM SPERMINE. THE COMPLEX WAS CRYSTALLIZED FROM 21 - 27% PEG 4000, 0.1 M CITRATE, PH 5.4 - 5.8, 20 MM NACL, 2 MM EDTA., pH 5.6, VAPOR DIFFUSION, HANGING DROP
PH range: 5.4-5.8
components of the solutions
IDNameCrystal IDSol ID
1EDTA11
2SPERMINE11
3PEG 400011
4NACL11
5SODIUM CITRATE11
6PEG 400012
Crystal grow
*PLUS
Temp: 4 ℃
Details: DNA:protein solution(in 2:1 ratio) was mixed with an equal volume of reservoir solution, Flick, K.E., (1997) Protein Sci., 6, 2677.
PH range low: 5.6 / PH range high: 5.4
Crystal grow comp
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
13 mg/mlI-PpoI1drop
220 mM1reservoirNaCl
32 mMEDTA1reservoir
40.1 Mcitrate1reservoir
521-27 %PEG40001reservoir
61

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: ALS BEAMLINE 5.0.2 / Synchrotron site: ALS / Beamline: 5.0.2
DetectorType: ADSC / Details: NONE / Detector: CCD / Collection date: Dec 15, 1997
RadiationMonochromator: DOUBLE CRYSTAL / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionD resolution high: 1.8 Å / D resolution low: 5 Å / Number obs: 362336 / Observed criterion sigma I: 2 / Rmerge I obs: 0.049 / Rsym value: 0.049 / NetI over sigmaI: 19.1 / Redundancy: 5.04 % / Percent possible obs: 99.8
Reflection shellRmerge I obs: 0.12 / Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / MeanI over sigI obs: 4.9 / Rsym value: 0.12 / Redundancy: 4.97 % / Percent possible all: 99.7
Reflection
*PLUS
Number obs: 71892 / Number measured all: 362336

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATA)data scaling
CCP4phasing
RefineMethod to determine structure: MIR / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 2
Displacement parametersB iso mean: 32.5 Å2
Least-squares processR factor R free: 0.297 / R factor R work: 0.208 / R factor obs: 0.208 / Highest resolution: 1.8 Å / Lowest resolution: 5 Å / Number reflection R free: 3581 / Number reflection obs: 71629 / Percent reflection R free: 5 / Percent reflection obs: 99.4
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 5 Å
Number of atoms included #LASTProtein: 2490 / Nucleic acid: 856 / Ligand: 6 / Solvent: 391 / Total: 3743
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints ncsNcs model details: RESTRAINTS
Refine LS shellHighest resolution: 1.8 Å / R factor R free: 0.412 / R factor R work: 0.336 / Lowest resolution: 1.87 Å / Number reflection R free: 352 / Number reflection R work: 7042 / Total number of bins used: 10 / Percent reflection R free: 5 / Percent reflection obs: 99.4
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDO.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION3TIP3P.PARAMETERTIP3P.TOPOLOGY
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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