1bsu

STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE

Method: X-RAY DIFFRACTION D_max: 83.1 Å Quality: GOOD

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

ENDONUCLEASE ECORV (3.1.21.4)

Escherichia coli

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 1–244 Chain B； UniProt 1–244	Not recorded	;DNA (5'-D(PAPAPGPAP(5CM)PIPTPCPTPT)-3') ; × 1 ;DNA (5'-D(APAPAPGPAP(5CM)PIPTPCPTP*T)-3') ; × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；293 K；pH 7.5, temperature 293K	Resolution 2.00 Å R-free 0.258

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 1BSU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AZ0 ECORV ENDONUCLEASE/DNA COMPLEX Deposited 1997-11-24	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 293.00K	Resolution 2.00 Å R-free 0.246
1AZ3 ECORV ENDONUCLEASE, UNLIGANDED, FORM B Deposited 1997-11-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.40 Å R-free 0.315
1AZ4 ECORV ENDONUCLEASE, UNLIGANDED, FORM B, T93A MUTANT Deposited 1997-11-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–245（244 aa） Chain B 2–245（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.40 Å R-free 0.337
1B94 RESTRICTION ENDONUCLEASE ECORV WITH CALCIUM Deposited 1999-02-19	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；pH 7.0, VAPOR DIFFUSION, SITTING DROP	Resolution 1.90 Å R-free 0.270
1B95 ANALYSIS OF A MUTATIONAL HOT-SPOT IN THE ECORV RESTRICTION ENDONUCLEASE: A CATALYTIC ROLE FOR A MAIN CHAIN CARBONYL GROUP Deposited 1999-02-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；pH 7.0, VAPOR DIFFUSION, SITTING DROP	Resolution 2.05 Å R-free 0.282
1B96 ANALYSIS OF A MUTATIONAL HOT-SPOT IN THE ECORV RESTRICTION ENDONUCLEASE: A CATALYTIC ROLE FOR A MAIN CHAIN CARBONYL GROUP Deposited 1999-02-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Mutation：Q69E Mutation：Q69E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；pH 7.0, VAPOR DIFFUSION, SITTING DROP	Resolution 2.30 Å R-free 0.282
1B97 ANALYSIS OF A MUTATIONAL HOT-SPOT IN THE ECORV RESTRICTION ENDONUCLEASE: A CATALYTIC ROLE FOR A MAIN CHAIN CARBONYL GROUP Deposited 1999-02-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Mutation：Q69L Mutation：Q69L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；pH 7.0, VAPOR DIFFUSION, SITTING DROP	Resolution 1.90 Å R-free 0.279
1BGB ECORV ENDONUCLEASE COMPLEX WITH 5'-CGGGATATCCC DNA Deposited 1998-05-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；CRYSTALLIZED FROM 15% PEG 4K, 100 MM IMIDAZOLE, (PH 6.5), 150 MM NACL., VAPOR DIFFUSION, HANGING DROP	Resolution 2.00 Å R-free 0.246
1BSS ECORV-T93A/DNA/CA2+ Deposited 1998-08-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Mutation：T93A Mutation：T93A	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.15 Å R-free 0.246
1BUA STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE Deposited 1998-09-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 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 2.15 Å R-free 0.288
1EO3 INHIBITION OF ECORV ENDONUCLEASE BY DEOXYRIBO-3'-S-PHOSPHOROTHIOLATES: A HIGH RESOLUTION X-RAY CRYSTALLOGRAPHIC STUDY Deposited 2000-03-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	MG MAGNESIUM ION × 4 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；25% PEG 4000, 0.1M HEPES, 0.15M NaCl, 50 mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.00 Å R-free 0.290
1EO4 ECORV BOUND TO MN2+ AND COGNATE DNA CONTAINING A 3'S SUBSTITION AT THE CLEAVAGE SITE Deposited 2000-03-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	MN MANGANESE (II) ION × 5 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；25% PEG 4000, 0.1M HEPES, 0.15M NaCl, 50 mM MnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.90 Å R-free 0.305
1EON ECORV BOUND TO 3'-S-PHOSPHOROTHIOLATE DNA AND CA2+ Deposited 2000-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	CL CHLORIDE ION × 4 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；25% PEG 4000, 0.1 M HEPES, 0.15 M NaCl, 50m M CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.60 Å R-free 0.281
1EOO ECORV BOUND TO COGNATE DNA Deposited 2000-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；297 K；1.5 M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.16 Å R-free 0.316
1EOP ECORV BOUND TO COGNATE DNA Deposited 2000-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；290 K；25% PEG 4000, 0.1 M acetate, 0.2 M tartrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.60 Å R-free 0.302
1RV5 COMPLEX OF ECORV ENDONUCLEASE WITH D(AAAGAT)/D(ATCTT) Deposited 1998-06-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.10 Å R-free 0.272
1RVA MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION Deposited 1994-10-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1RVB MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION Deposited 1994-10-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1RVC MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION Deposited 1994-10-21	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 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1RVE THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA FRAGMENTS Deposited 1992-02-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1STX Structure of the K38A mutant of EcoRV bound to cognate DNA and Mn2+ Deposited 2004-03-25	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 1–244（244 aa） Chain B 1–244（244 aa）	Mutation：K38A Mutation：K38A	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；290 K；17% PEG 4000, 0.1M HEPES pH 7.5, 0.15M NaCl 50mM MnCl2, Vapor diffusion, temperature 290K	Resolution 2.10 Å R-free 0.262
1SUZ The structure of K92A EcoRV bound to cognate DNA and Mg2+ Deposited 2004-03-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Mutation：K92A Mutation：K92A	MG MAGNESIUM ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；17% PEG 4K, 0.1M tartrate, 0.1M HPETES, 50mM MgCl2, pH 7.5, VAPOR DIFFUSION, temperature 22K	Resolution 1.80 Å R-free 0.244
1SX5 K38A EcoRV bound to cleaved DNA and Mn2+: P1 crystal form Deposited 2004-03-30	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 1–244（244 aa） Chain B 1–244（244 aa）	Mutation：K38A Mutation：K38A	MN MANGANESE (II) ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；315 K；PEG 4000, 0.1M HEPES, 0.15M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 315K	Resolution 1.50 Å R-free 0.254
1SX8 EcoRV bound to cognate DNA and Mn2+ Deposited 2004-03-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Mutation：K92A Mutation：K92A	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；PEG 4000, 0.1M HEPES, 0.15M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 2.15 Å R-free 0.254
2B0D EcoRV Restriction Endonuclease/GAATTC/Ca2+ Deposited 2005-09-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 0–244（245 aa） Chain B 0–244（245 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；297 K；PEG 4K, Hepes, NaCl, CaCl2, Glycerol, pH 7.5, vapor diffusion, hanging drop, temperature 297K	Resolution 2.00 Å R-free 0.302
2B0E EcoRV Restriction Endonuclease/GAAUTC/Ca2+ Deposited 2005-09-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 0–244（245 aa） Chain B 0–244（245 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；297 K；PEG 4K, Hepes, NaCl, CaCl2, pH 7.5, vapor diffusion, hanging drop, temperature 297K	Resolution 1.90 Å R-free 0.314
2GE5 EcoRV Restriction Endonuclease C-terminal deletion mutant/GATATC/Ca2+ Deposited 2006-03-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–219（219 aa） Fragment：residues 1-219 Chain B 1–219（219 aa） Fragment：residues 1-219	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；250 mM NaCl, 8-12% PEG 4k, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.40 Å R-free 0.284
2RVE THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS Deposited 1991-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–244（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；pH 6.00, VAPOR DIFFUSION	Resolution 3.00 Å
2RVE THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS Deposited 1991-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–244（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；pH 6.00, VAPOR DIFFUSION	Resolution 3.00 Å
4RVE THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS Deposited 1993-02-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–244（244 aa） Chain B 1–244（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；pH 7.00, VAPOR DIFFUSION	Resolution 3.00 Å
4RVE THE CRYSTAL STRUCTURE OF ECORV ENDONUCLEASE AND OF ITS COMPLEXES WITH COGNATE AND NON-COGNATE DNA SEGMENTS Deposited 1993-02-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 1–244（244 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；pH 7.00, VAPOR DIFFUSION	Resolution 3.00 Å
5F8A Crystal structure of the ternary EcoRV-DNA-Lu complex with uncleaved DNA substrate. Lanthanide binding to EcoRV-DNA complex inhibits cleavage. Deposited 2015-12-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–245（244 aa） Chain B 2–245（244 aa）	Not recorded	LU LUTETIUM (III) ION × 2 NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；285 K；4.5 mg/mL (monomer), protein(dimer):DNA - 1:1, Enzyme:Well - 3uL:3uL, Well - 500uL of 100 mM HEPES pH 7.4, 8% Ethylene glycol, 4% Polyethylene glycol 8000, 10% glycerol.	Resolution 1.76 Å R-free 0.199
5HLK Crystal structure of the ternary EcoRV-DNA-Lu complex with cleaved DNA substrate. Deposited 2016-01-15	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 2–245（244 aa） Chain B 2–245（244 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 7 NA SODIUM ION × 4 LU LUTETIUM (III) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；9.4 mg/mL, 3:3 Enzyme:Well, 100 mM HEPES pH 7.5, 8% Ethylene glycol, 7% Polyethylene glycol 8000, 10% glycerol	Resolution 2.00 Å R-free 0.228

31 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	T2E5_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–244； UniProt 1–244 Author chain B； PDBConstruct 1–244； UniProt 1–244

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bsu
Deposition date deposition_date	1998-08-30
Structure title title	STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE
Keywords keywords	COMPLEX ENDONUCLEASE ECORV (3.1.21.4)-DNA, HYDROLASE-DNA COMPLEX; HYDROLASE/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	23.74 Å
Radius of gyration Rg (electron density) rg_electron	23.23 Å
Forward intensity I(0) i0	59123900.00
Molecular weight molecular_weight	57591.0 kDa
Excluded volume excluded_volume	70757 Å³
Envelope volume envelope_volume	82641 Å³
Hydration-shell volume shell_volume	29198 Å³
Envelope diameter envelope_diameter	80.9 Å
Shell Rg shell_rg	30.68 Å
Envelope Rg envelope_rg	23.36 Å
Shape Rg shape_rg	23.26 Å
Total Rg total_rg	23.90 Å
Total atoms total_atoms	4063
Residues n_residues	484
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	83.1 Å
Rg (real space) rg_real	23.64 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	5.9120e+07
I(0) uncertainty (real space) i0_real_error	9.6360e+05
Rg (reciprocal space) rg_reciprocal	23.66 Å
I(0) (reciprocal space) i0_reciprocal	59120000.0000
Solution quality estimate total_estimate	0.7714
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	29.9 Å
Skewness Skewness skewness	0.264
Kurtosis Kurtosis kurtosis	-0.332
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15040000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.686; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(PAPAPGPAP(5CM)PIPTPCPTPT)-3') ;
Molecular weight formula_weight	3043.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	4281

AAGACITCTT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APAPAPGPAP(5CM)PIPTPCPTP*T)-3') ;
Molecular weight formula_weight	3356.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

AAAGACITCTT

Entity 3 Entity 3 polymer

Description description	ENDONUCLEASE ECORV (3.1.21.4)
Molecular weight formula_weight	28559.2 kDa
EC 编号 ec_number	3.1.21.4
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFELFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	218

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bsua_
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.52.1.2 — Restriction endonuclease EcoRV

Domain ID domain_id	d1bsub_
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.52.1.2 — Restriction endonuclease EcoRV

CATH v4.4 (2 domains)

Domain ID domain_id	1bsuA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	600 — ECO RV Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — DNA mismatch repair MutH/Restriction endonuclease, type II

Domain ID domain_id	1bsuB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	600 — ECO RV Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — DNA mismatch repair MutH/Restriction endonuclease, type II

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8. Citations (3)

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Unit-cell length a length_a	50.300 Å
Unit-cell length b length_b	64.000 Å
Unit-cell length c length_c	49.100 Å
Unit-cell angle α angle_alpha	109.10 °
Unit-cell angle β angle_beta	108.10 °
Unit-cell angle γ angle_gamma	96.50 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1830
R_work r_work	0.1830
R_free r_free	0.2580

fit	/app/data/saxs_computation/bs/1bsu/1bsu.fit
pddf	/app/data/pr_computation/bs/1bsu/1bsu.pr.out
profile	/app/data/saxs_computation/bs/1bsu/1bsu.dat

STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE

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

ENDONUCLEASE ECORV (3.1.21.4)

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)