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- PDB-1eri: X-RAY STRUCTURE OF THE DNA-ECO RI ENDONUCLEASE-DNA RECOGNITION CO... -

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Basic information

Entry
Database: PDB / ID: 1eri
TitleX-RAY STRUCTURE OF THE DNA-ECO RI ENDONUCLEASE-DNA RECOGNITION COMPLEX: THE RECOGNITION NETWORK AND THE INTEGRATION OF RECOGNITION AND CLEAVAGE
Components
  • DNA (5'-D(*TP*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
  • PROTEIN (ECO RI ENDONUCLEASE (E.C.3.1.21.4))
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / magnesium ion binding / DNA binding
Similarity search - Function
Restriction endonuclease, type II, EcoRI / Restriction endonuclease, type II, EcoRI, Proteobacteria / Restriction endonuclease EcoRI / ECO RI Endonuclease; Chain A / Eco RI Endonuclease, subunit A / Restriction endonuclease, type II, EcoRI/MunI / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Type II restriction enzyme EcoRI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsKim, Y. / Grable, J.C. / Love, R. / Greene, P.J. / Rosenberg, J.M.
Citation
Journal: Science / Year: 1990
Title: Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing.
Authors: Kim, Y.C. / Grable, J.C. / Love, R. / Greene, P.J. / Rosenberg, J.M.
#1: Journal: To be Published
Title: Preliminary Characterization of EcoRI-DNA Co-Crystals: Incomplete Factorial Design of Oligonucleotide Sequences
Authors: Wilkosz, P.A. / Chandrasekhar, K. / Rosenberg, J.M.
#2: Journal: To be Published
Title: Molecular Dynamics Simulations Suggest that the EcoRI Kink is an Example of Molecular Strain
Authors: Kumar, S. / Duan, Y. / Kollman, P.A. / Rosenberg, J.M.
#3: Journal: Structural Biology: The State of the Art; Proceedings of the Eighth Conversation, State University of New York, Albany
Year: 1994
Title: Studies on the Canonical DNA-EcoRI Endonuclease Complex and the EcoRI Kink
Authors: Kim, Y. / Choi, J. / Grable, J.C. / Greene, P. / Hager, P. / Rosenberg, J.M.
#4: Journal: Curr.Opin.Struct.Biol. / Year: 1991
Title: Structure and Function of Restriction Endonucleases
Authors: Rosenberg, J.M.
History
DepositionMay 18, 1994Deposition site: BNL / Processing site: BNL
SupersessionFeb 7, 1995ID: 1R1E
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*TP*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
A: PROTEIN (ECO RI ENDONUCLEASE (E.C.3.1.21.4))


Theoretical massNumber of molelcules
Total (without water)34,9382
Polymers34,9382
Non-polymers00
Water1,09961
1
B: DNA (5'-D(*TP*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
A: PROTEIN (ECO RI ENDONUCLEASE (E.C.3.1.21.4))

B: DNA (5'-D(*TP*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
A: PROTEIN (ECO RI ENDONUCLEASE (E.C.3.1.21.4))


Theoretical massNumber of molelcules
Total (without water)69,8764
Polymers69,8764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)118.400, 118.400, 49.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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


Mass: 3967.585 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (ECO RI ENDONUCLEASE (E.C.3.1.21.4))


Mass: 30970.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P00642
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277 K / Details: 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 40011
3WATER12
4PEG 40012
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Details: Grable J., (1984) J. Biomol. Struct. Dyn., 1, 1149.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.7 mg/mlenzyme1drop
22.8 mg/mlDNA1drop
38 %(w/v)PEG4001drop
440 mMBis-Tris propane1reservoir
51 mMEDTA1reservoir
616 %PEG4001reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.7 Å / Num. obs: 8775 / % possible obs: 60 % / Observed criterion σ(I): 3
Reflection
*PLUS
Highest resolution: 2.7 Å / % possible obs: 60 % / Observed criterion σ(I): 3

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Processing

Software
NameClassification
X-PLORrefinement
PROLSQrefinement
RefinementResolution: 2.5→8 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.28 --
Rwork0.17 --
obs0.17 8319 60 %
Displacement parametersBiso mean: 26.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 263 0 61 2375
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.58
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.58
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1
X-RAY DIFFRACTIONp_mcangle_it1.5
X-RAY DIFFRACTIONp_scbond_it1.5
X-RAY DIFFRACTIONp_scangle_it2
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(F): 3 / Rfactor obs: 0.17 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_d1.58
X-RAY DIFFRACTIONp_dihedral_angle_d25.6
X-RAY DIFFRACTIONp_improper_angle_d1.55

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