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- PDB-1eo3: INHIBITION OF ECORV ENDONUCLEASE BY DEOXYRIBO-3'-S-PHOSPHOROTHIOL... -

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Basic information

Entry
Database: PDB / ID: 1eo3
TitleINHIBITION OF ECORV ENDONUCLEASE BY DEOXYRIBO-3'-S-PHOSPHOROTHIOLATES: A HIGH RESOLUTION X-RAY CRYSTALLOGRAPHIC STUDY
Components
  • DNA (5'-D(*CP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)-3')
  • TYPE II RESTRICTION ENZYME ECORV
Keywordshydrolase/DNA / Protein-DNA complex / restriction endonuclease / DNA analog / hydrolase-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / metal ion binding
Similarity search - Function
Restriction endonuclease, type II, EcoRV / Restriction endonuclease, type II, EcoRV, Proteobacteria / Restriction endonuclease EcoRV / DNA mismatch repair MutH/Restriction endonuclease, type II / DNA mismatch repair MutH/Type II restriction endonuclease superfamily / ECO RV Endonuclease; Chain A / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / DNA / DNA (> 10) / Type II restriction enzyme EcoRV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHorton, N.C. / Connolly, B.A. / Perona, J.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2000
Title: Inhibition of EcoRV Endonuclease by Deoxyribo-3'-S-phosphorothiolates: A High-Resolution X-ray Crystallographic Study
Authors: Horton, N.C. / Connolly, B.A. / Perona, J.J.
History
DepositionMar 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 31, 2019Group: Data collection / Derived calculations / Category: chem_comp / struct_conn / Item: _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / 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 / _entity_poly.pdbx_seq_one_letter_code_can / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*CP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)-3')
D: DNA (5'-D(*CP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)-3')
A: TYPE II RESTRICTION ENZYME ECORV
B: TYPE II RESTRICTION ENZYME ECORV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,29510
Polymers64,0774
Non-polymers2176
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.0, 48.5, 63.8
Angle α, β, γ (deg.)97.0, 108.9, 106.3
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
DetailsThe biological assembly is a dimer composed of chains A and B / The biological assembly is a duplex composed of strands C and D

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Components

#1: DNA chain DNA (5'-D(*CP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)-3')


Mass: 3348.276 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein TYPE II RESTRICTION ENZYME ECORV / E.C.3.1.21.4 / ENDONUCLEASE ECORV / R.ECORV


Mass: 28690.354 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)
References: UniProt: P04390, type II site-specific deoxyribonuclease
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 4000, 0.1M HEPES, 0.15M NaCl, 50 mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2NaCl11
3MgCl211
4PEG 400011
5PEG 400012
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlEcoRV1drop
21.0 mg/mlDNA1drop
3100 mMHEPES1reservoir
4150 mM1reservoirNaCl
510-15 %PEG40001reservoir
650 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 31662 / Num. obs: 31662 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 1.77 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 7.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.358 / Num. unique all: 4498 / % possible all: 90.5
Reflection
*PLUS
Num. measured all: 55892
Reflection shell
*PLUS
% possible obs: 90.5 % / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
X-PLORmodel building
X-PLORrefinement
CCP4(TRUNCATE)data scaling
X-PLORphasing
RefinementResolution: 2→4.9 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: X-Plor
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1514 6 %random
Rwork0.196 ---
all0.2 29583 --
obs0.2 29583 92.5 %-
Refinement stepCycle: LAST / Resolution: 2→4.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 410 4 305 4533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg2.12
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 4.9 Å / σ(F): 2 / % reflection Rfree: 6 % / Rfactor obs: 0.196 / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.2 Å2

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