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2oxv

Structure of the A138T promiscuous mutant of the EcoRI restriction endonuclease bound to its cognate recognition site.

Method: X-RAY DIFFRACTION Dmax: 74.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Type II restriction enzyme EcoRI

Escherichia coli

UniProt P00642

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain A； UniProt 1–277 Mutation：A138T ;DNA (5'-D(*TP*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') ; × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.15 K；cryoprotectant solution is 40mM bis-tris Propane, 16% v/v PEG 400, 15% v/v glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K Resolution 1.95 Å R-free 0.244

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2OXV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CKQ PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAATTCGCG) COMPLEX Deposited 1999-04-22 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–276（276 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；pH 7.5, VAPOR DIFFUSION, HANGING DROP
Resolution 1.85 Å R-free 0.286
1CL8 A PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAPTTCGCG) COMPLEX WITH DNA BASE ANALOG PURINE (P) Deposited 1999-05-06 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–276（276 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；pH 7.5, VAPOR DIFFUSION, HANGING DROP
Resolution 1.80 Å R-free 0.287
1ERI X-RAY STRUCTURE OF THE DNA-ECO RI ENDONUCLEASE-DNA RECOGNITION COMPLEX: THE RECOGNITION NETWORK AND THE INTEGRATION OF RECOGNITION AND CLEAVAGE Deposited 1994-05-18 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–276（276 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；277.00K
Resolution 2.50 Å R-free 0.280
1QC9 THE CRYSTALLOGRAPHIC STRUCTURE OF RESTRICTION ENDONUCLEASE ECO RI AT 3.3 A IN THE ABSENSE OF DNA Deposited 1999-05-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–277（276 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.295
1QC9 THE CRYSTALLOGRAPHIC STRUCTURE OF RESTRICTION ENDONUCLEASE ECO RI AT 3.3 A IN THE ABSENSE OF DNA Deposited 1999-05-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 2–277（276 aa）
Chain C 2–277（276 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.295
1QPS THE CRYSTAL STRUCTURE OF A POST-REACTIVE COGNATE DNA-ECO RI COMPLEX AT 2.50 A IN THE PRESENCE OF MN2+ ION Deposited 1999-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 16–276（261 aa） Fragment：RESIDUES 17-277
Not recorded MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；MN ION WAS SOAKED INTO PRE-REACTIVE PROTEIN-DNA COCRYSTALS AND DNA CLEAVAGE OCCURED IN-CRYSTALLO, pH 7.5, VAPOR DIFFUSION, temperature 4K
Resolution 2.50 Å
1QRH X-RAY STRUCTURE OF THE DNA-ECO RI ENDONUCLEASE COMPLEXES WITH AN R145K MUTATION AT 2.7 A Deposited 1999-06-14 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 16–276（261 aa） Fragment：RESIDUES 17-277
Mutation：ARG145LYS No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PRECIPITANT: 15% PEG 400, 40 MM BTP, PH 7.1; RESERVOIR: 15% PEG 3350; 40 MM BTP; PH 6.5; DROP:3 UL PROTEIN, 2 UL DNA, 1.5 UL PPT, VAPOR DIFFUSION, SITTING DROP
Resolution 2.50 Å
1QRI X-RAY STRUCTURE OF THE DNA-ECO RI ENDONUCLEASE COMPLEXES WITH AN E144D MUTATION AT 2.7 A Deposited 1999-06-14 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 16–276（261 aa） Fragment：RESIDUES 17-277
Mutation：GLU144ASP No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；PRECIPITANT: 40% PEG 400; 40 MM BTP; PH 8.0; RESERVOIR: 16% PEG 400; 40 MM BTP; PH 6.5; DROP: 5 UL PROTEIN, 2 UL DNA, 1 UL PPT, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.60 Å

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name T2E1_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–277； UniProt 1–277

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2oxv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2oxv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2oxv
Deposition date deposition_date2007-02-21
Structure title titleStructure of the A138T promiscuous mutant of the EcoRI restriction endonuclease bound to its cognate recognition site.
Keywords keywords;EcoRI, type II restriction endonuclease, protein-DNA interactions, promiscuous mutant, relaxed specificity mutant, hydrolase-DNA COMPLEX ;; hydrolase/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.35 Å
Radius of gyration Rg (electron density) rg_electron21.26 Å
Forward intensity I(0) i022093600.00
Molecular weight molecular_weight33125.0 kDa
Excluded volume excluded_volume40412 ų
Envelope volume envelope_volume50053 ų
Hydration-shell volume shell_volume20306 ų
Envelope diameter envelope_diameter74.7 Å
Shell Rg shell_rg27.45 Å
Envelope Rg envelope_rg21.65 Å
Shape Rg shape_rg21.24 Å
Total Rg total_rg22.13 Å
Total atoms total_atoms2316
Residues n_residues274
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax74.0 Å
Rg (real space) rg_real22.33 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real2.2090e+07
I(0) uncertainty (real space) i0_real_error3.0900e+05
Rg (reciprocal space) rg_reciprocal22.34 Å
I(0) (reciprocal space) i0_reciprocal22090000.0000
Solution quality estimate total_estimate0.8951
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.8 Å
Skewness Skewness skewness0.328
Kurtosis Kurtosis kurtosis-0.290
Angular range angular_range— – 0.3550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2544000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.996
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2oxva_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.52 — Restriction endonuclease-like
Superfamily Superfamily superfamilyc.52.1 — Restriction endonuclease-like
Family Family familyc.52.1.1 — Restriction endonuclease EcoRI

CATH v4.4 (1 domains)

Domain ID domain_id2oxvA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology580 — ECO RI Endonuclease; Chain A
Homologous superfamily homologous superfamily10 — Eco RI Endonuclease, subunit A
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8. Citations (1)

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9. Files and Curves (10)