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- PDB-7e8r: EcoT38I restriction endonuclease -

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Basic information

Entry
Database: PDB / ID: 7e8r
TitleEcoT38I restriction endonuclease
ComponentsEcoT38I restriction endonuclease
KeywordsDNA BINDING PROTEIN / Endonuclease
Function / homologyRestriction endonuclease, type II, SacI / SacI restriction endonuclease / endonuclease activity / metal ion binding / EcoT38I restriction endonuclease
Function and homology information
Biological speciesEscherichia phage P2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKita, K. / Mikami, B.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16380061 Japan
CitationJournal: To Be Published
Title: Structural analysis of EcoT38I restriction endonuclease
Authors: Kita, K. / Mikami, B.
History
DepositionMar 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EcoT38I restriction endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,86511
Polymers38,9441
Non-polymers92110
Water4,936274
1
A: EcoT38I restriction endonuclease
hetero molecules

A: EcoT38I restriction endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,73122
Polymers77,8892
Non-polymers1,84220
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area6450 Å2
ΔGint-22 kcal/mol
Surface area31490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.159, 53.159, 250.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein EcoT38I restriction endonuclease


Mass: 38944.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage P2 (virus) / Gene: ecoT38IR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q83VS8
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.02 % / Description: thin plate
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG6000, 5% MPD, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 33635 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 29.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.059 / Net I/σ(I): 25.6
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.46 / Num. unique obs: 5245 / CC1/2: 0.936 / Rrim(I) all: 0.4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BSSdata collection
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→43.2 Å / SU ML: 0.2261 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2413 1680 5 %
Rwork0.1996 31946 -
obs0.2017 33626 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 60 274 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652845
X-RAY DIFFRACTIONf_angle_d0.73533857
X-RAY DIFFRACTIONf_chiral_restr0.0538452
X-RAY DIFFRACTIONf_plane_restr0.0043488
X-RAY DIFFRACTIONf_dihedral_angle_d18.95191048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.29971320.28392534X-RAY DIFFRACTION98.12
1.95-2.020.29481370.24892607X-RAY DIFFRACTION100
2.02-2.090.28721380.22772606X-RAY DIFFRACTION100
2.09-2.170.25331370.2222616X-RAY DIFFRACTION100
2.17-2.270.25521390.2182630X-RAY DIFFRACTION100
2.27-2.390.25591390.22072639X-RAY DIFFRACTION100
2.39-2.540.28721390.21322654X-RAY DIFFRACTION100
2.54-2.740.29281390.21882638X-RAY DIFFRACTION100
2.74-3.010.25161410.21232675X-RAY DIFFRACTION100
3.01-3.450.23611410.1932688X-RAY DIFFRACTION100
3.45-4.340.19721450.17022744X-RAY DIFFRACTION100
4.34-43.20.22121530.18112915X-RAY DIFFRACTION99.87

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