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- PDB-1wtd: Crystal structure of type II restrcition endonuclease, EcoO109I D... -

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Basic information

Entry
Database: PDB / ID: 1wtd
TitleCrystal structure of type II restrcition endonuclease, EcoO109I DNA-free form
ComponentsEcoO109IR
KeywordsHYDROLASE / RESTRICTION ENDONUCLEASE / DNA-FREE FROM
Function / homology
Function and homology information


type ii restriction endonuclease, domain 1 / type ii restriction endonuclease, domain 1 / type ii restriction endonuclease, domain 2 / type ii restriction endonuclease, domain 2 / Restriction endonuclease EcoO109IR, catalytic domain superfamily / Restriction endonuclease type II-like / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.401 Å
AuthorsHashimoto, H. / Shimizu, T. / Imasaki, T. / Kato, M. / Shichijo, N. / Kita, K. / Sato, M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA
Authors: Hashimoto, H. / Shimizu, T. / Imasaki, T. / Kato, M. / Shichijo, N. / Kita, K. / Sato, M.
History
DepositionNov 22, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: EcoO109IR
B: EcoO109IR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,88512
Polymers62,9642
Non-polymers92110
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-38 kcal/mol
Surface area24250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.551, 175.551, 44.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein EcoO109IR / TYPE II RESTRICTION ENDONUCLEASE


Mass: 31481.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: Q9RPJ3, type II site-specific deoxyribonuclease
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, potassium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.0000, 1.0082, 1.0089, 0.9
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.00821
31.00891
40.91
ReflectionResolution: 2.4→20 Å / Num. all: 26765 / Num. obs: 26765 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.401→20 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.896 / Cross valid method: THROUGHOUT / ESU R: 0.441 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1343 5 %RANDOM
Rwork0.255 ---
all0.257 25421 --
obs0.257 25421 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.495 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å20 Å2
2--2.09 Å20 Å2
3----4.18 Å2
Refinement stepCycle: LAST / Resolution: 2.401→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4125 0 60 45 4230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214268
X-RAY DIFFRACTIONr_bond_other_d00.023781
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9385776
X-RAY DIFFRACTIONr_angle_other_deg3.84538736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7855527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.51925.127197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.62615684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4691512
X-RAY DIFFRACTIONr_chiral_restr0.080.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024759
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02847
X-RAY DIFFRACTIONr_nbd_refined0.2110.21001
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22086
X-RAY DIFFRACTIONr_nbtor_other0.1150.21966
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2122
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2770.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1050.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.180.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7021.52633
X-RAY DIFFRACTIONr_mcbond_other01.51086
X-RAY DIFFRACTIONr_mcangle_it1.27224182
X-RAY DIFFRACTIONr_scbond_it1.68631635
X-RAY DIFFRACTIONr_scangle_it2.6434.51594
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 92 -
Rwork0.327 1883 -
obs--98.41 %

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