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1qc9

THE CRYSTALLOGRAPHIC STRUCTURE OF RESTRICTION ENDONUCLEASE ECO RI AT 3.3 A IN THE ABSENSE OF DNA

Method: X-RAY DIFFRACTION Dmax: 159.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (ECO RI ENDONUCLEASE)

OrganismNot specified

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 2–277 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å R-free 0.295
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 2–277 Chain C； UniProt 2–277 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 Å R-free 0.295

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 1QC9 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 oligomeric state 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 oligomeric state 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 oligomeric state 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
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 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 oligomeric state 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 oligomeric state 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
2OXV Structure of the A138T promiscuous mutant of the EcoRI restriction endonuclease bound to its cognate recognition site. Deposited 2007-02-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–277（277 aa）
Mutation：A138T No recorded non-water small molecule 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

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

View Construct and Data Evidence
UniProt name T2E1_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–276； UniProt 2–277 Author chain B； PDBConstruct 1–276； UniProt 2–277 Author chain C； PDBConstruct 1–276； UniProt 2–277

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 1qc9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1qc9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1qc9
Deposition date deposition_date1999-05-18
Structure title titleTHE CRYSTALLOGRAPHIC STRUCTURE OF RESTRICTION ENDONUCLEASE ECO RI AT 3.3 A IN THE ABSENSE OF DNA
Keywords keywordsPROTEIN, RESTRICTION ENDONUCLEASE, APOENZYME, ENDONUCLEASE; ENDONUCLEASE
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_guinier56.33 Å
Radius of gyration Rg (electron density) rg_electron56.30 Å
Forward intensity I(0) i0103982000.00
Molecular weight molecular_weight84928.0 kDa
Excluded volume excluded_volume106390 ų
Envelope volume envelope_volume201590 ų
Hydration-shell volume shell_volume30690 ų
Envelope diameter envelope_diameter158.9 Å
Shell Rg shell_rg60.51 Å
Envelope Rg envelope_rg51.07 Å
Shape Rg shape_rg56.32 Å
Total Rg total_rg56.37 Å
Total atoms total_atoms5979
Residues n_residues759
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 dmax159.7 Å
Rg (real space) rg_real56.12 Å
Rg uncertainty (real space) rg_real_error1.57 Å
I(0) (real space) i0_real1.0400e+08
I(0) uncertainty (real space) i0_real_error1.9340e+06
Rg (reciprocal space) rg_reciprocal56.45 Å
I(0) (reciprocal space) i0_reciprocal104000000.0000
Solution quality estimate total_estimate0.6027
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary96.9 Å
Skewness Skewness skewness-0.354
Kurtosis Kurtosis kurtosis-1.208
Angular range angular_range— – 0.1400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2973000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.027; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.750; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1qc9a_
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
Domain ID domain_idd1qc9b_
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
Domain ID domain_idd1qc9c_
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 (3 domains)

Domain ID domain_id1qc9A00
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
Domain ID domain_id1qc9B00
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
Domain ID domain_id1qc9C00
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)