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- PDB-1u3e: DNA binding and cleavage by the HNH homing endonuclease I-HmuI -

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Basic information

Entry
Database: PDB / ID: 1u3e
TitleDNA binding and cleavage by the HNH homing endonuclease I-HmuI
Components
  • 36-MER
  • 5'-D(*CP*TP*TP*AP*CP*GP*TP*GP*GP*GP*AP*AP*TP*TP*GP*CP*TP*GP*AP*GP*C)-3'
  • 5'-D(P*GP*TP*TP*AP*GP*GP*CP*TP*CP*AP*TP*TP*AP*CP*T)-3'
  • HNH homing endonuclease
KeywordsDNA binding protein/DNA / HNH catalytic motif / Helix-turn-helix DNA binding domain / protein-DNA complex / DNA binding protein-DNA COMPLEX
Function / homology
Function and homology information


intron homing / endonuclease activity / Hydrolases; Acting on ester bonds
Similarity search - Function
Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A - #20 / Intron encoded nuclease repeat / NUMOD4 / NUMOD4 motif / HNH endonuclease / Intron encoded nuclease repeat motif / Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A / HNH nucleases / HNH nuclease / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A - #20 / Intron encoded nuclease repeat / NUMOD4 / NUMOD4 motif / HNH endonuclease / Intron encoded nuclease repeat motif / Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A / HNH nucleases / HNH nuclease / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / STRONTIUM ION / DNA / DNA (> 10) / DNA endonuclease I-HmuI
Similarity search - Component
Biological speciesBacillus phage SPO1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.92 Å
AuthorsShen, B.W. / Landthaler, M. / Shub, D.A. / Stoddard, B.L.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: DNA Binding and Cleavage by the HNH Homing Endonuclease I-HmuI.
Authors: Shen, B.W. / Landthaler, M. / Shub, D.A. / Stoddard, B.L.
History
DepositionJul 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 400COMPOUND The nick between Chain B and C was created by the enzyme

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 36-MER
B: 5'-D(*CP*TP*TP*AP*CP*GP*TP*GP*GP*GP*AP*AP*TP*TP*GP*CP*TP*GP*AP*GP*C)-3'
C: 5'-D(P*GP*TP*TP*AP*GP*GP*CP*TP*CP*AP*TP*TP*AP*CP*T)-3'
M: HNH homing endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,87417
Polymers41,9124
Non-polymers96213
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.000, 108.300, 248.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-415-

SR

Detailsone biological assembly per asymmetric unit

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Components

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DNA chain , 3 types, 3 molecules ABC

#1: DNA chain 36-MER


Mass: 11039.131 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*TP*TP*AP*CP*GP*TP*GP*GP*GP*AP*AP*TP*TP*GP*CP*TP*GP*AP*GP*C)-3'


Mass: 6494.194 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*GP*TP*TP*AP*GP*GP*CP*TP*CP*AP*TP*TP*AP*CP*T)-3'


Mass: 4574.982 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules M

#4: Protein HNH homing endonuclease


Mass: 19803.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SPO1 (virus) / Genus: SPO1-like viruses / Gene: bacteriophage SP01 / Plasmid: pKYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+ / References: UniProt: P34081

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Non-polymers , 5 types, 44 molecules

#5: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Sr
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: hanging drop vapor diffusion / pH: 8.75
Details: PEG600, pH 8.75, Hanging drop vapor diffusion, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG60011
2H2O11
3PEG60012
4PEG60012

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.210.9796
SYNCHROTRONALS 5.0.121
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDDec 10, 2003toroidal focusing mirror
ADSC QUANTUM 2102CCDDec 10, 2003mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystal Si(111), cylindrically bentSINGLE WAVELENGTHMx-ray1
2double crystal Si(220)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
211
ReflectionResolution: 2.9→50 Å / Num. all: 13440 / Num. obs: 13360 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rsym value: 0.065 / Net I/σ(I): 23.3
Reflection shellResolution: 2.9→2.96 Å / Redundancy: 4 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.4 / Num. unique all: 717 / Rsym value: 0.433 / % possible all: 97

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: SAD
Starting model: pdb from SAD phase and DM with solvent flipping

Resolution: 2.92→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2174 -random
Rwork0.216 ---
all0.22 13440 --
obs0.22 13360 10 %-
Displacement parametersBiso mean: 68.65 Å2
Baniso -1Baniso -2Baniso -3
1-6.855 Å20 Å20 Å2
2---14.829 Å20 Å2
3---7.974 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.92→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 1471 41 31 2936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.267
X-RAY DIFFRACTIONc_bond_d0.0066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID
2.92-3.020.4651590.428X-RAY DIFFRACTION
3.02-3.150.41281220.363X-RAY DIFFRACTION

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