SAXSdb — 1cl8

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (ENDONUCLEASE)

OrganismNot specified

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 1–276	Not recorded	;DNA (5'-D(TPCPGPCPGPAP(PRN)PTPTPCPGPCP*G)-3') ; × 2	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

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 1CL8	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 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
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 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 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 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
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 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 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 1–276； UniProt 1–276

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cl8
Deposition date deposition_date	1999-05-06
Structure title title	A PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAPTTCGCG) COMPLEX WITH DNA BASE ANALOG PURINE (P)
Keywords keywords	ENDONUCLEASE/DNA, DNA BASE ANALOG, PROTEIN-DNA COMPLEX; PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.54 Å
Radius of gyration Rg (electron density) rg_electron	21.44 Å
Forward intensity I(0) i0	21988400.00
Molecular weight molecular_weight	33080.0 kDa
Excluded volume excluded_volume	40369 Å³
Envelope volume envelope_volume	50505 Å³
Hydration-shell volume shell_volume	20393 Å³
Envelope diameter envelope_diameter	77.9 Å
Shell Rg shell_rg	27.61 Å
Envelope Rg envelope_rg	21.82 Å
Shape Rg shape_rg	21.42 Å
Total Rg total_rg	22.30 Å
Total atoms total_atoms	2313
Residues n_residues	273
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	76.6 Å
Rg (real space) rg_real	22.53 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	2.1990e+07
I(0) uncertainty (real space) i0_real_error	2.9300e+05
Rg (reciprocal space) rg_reciprocal	22.53 Å
I(0) (reciprocal space) i0_reciprocal	21990000.0000
Solution quality estimate total_estimate	0.8823
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.5 Å
Skewness Skewness skewness	0.337
Kurtosis Kurtosis kurtosis	-0.271
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2582000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.958

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(TPCPGPCPGPAP(PRN)PTPTPCPGPCP*G)-3') ;
Molecular weight formula_weight	3952.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	2471

TCGCGAATTCGCG

Entity 2 Entity 2 polymer

Description description	PROTEIN (ENDONUCLEASE)
Molecular weight formula_weight	30970.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

SNKKQSNRLTEQHKLSQGVIGIFGDYAKAHDLAVGEVSKLVKKALSNEYPQLSFRYRDSIKKTEINEALKKIDPDLGGTLFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDIINIRNGLLVGKRGDQDLMAAGNAIERSHKNISEIANFMLSESHFPYVLFLEGSNFLTENISITRPDGRVVNLEYNSGILNRLDRLTAANYGMPINSNLCINKFVNHKDKSIMLQAASIYTQGDGREWDSKIMFEIMFDISTTSLRVLGRDLFEQLTSK

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	155

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cl8a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.1 — Restriction endonuclease-like
Family Family family	c.52.1.1 — Restriction endonuclease EcoRI

CATH v4.4 (1 domains)

Domain ID domain_id	1cl8A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	580 — ECO RI Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Eco RI Endonuclease, subunit A

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8. Citations (1)

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Unit-cell length a length_a	117.833 Å
Unit-cell length b length_b	117.833 Å
Unit-cell length c length_c	48.989 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2430
R_work r_work	0.2430
R_free r_free	0.2870

fit	/app/data/saxs_computation/cl/1cl8/1cl8.fit
pddf	/app/data/pr_computation/cl/1cl8/1cl8.pr.out
profile	/app/data/saxs_computation/cl/1cl8/1cl8.dat

A PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAPTTCGCG) COMPLEX WITH DNA BASE ANALOG PURINE (P)

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (ENDONUCLEASE)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)