SAXSdb — 2vbl

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

DNA ENDONUCLEASE I-CREI

CHLAMYDOMONAS REINHARDTII

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 4 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 1–153 Chain B； UniProt 1–153	Fragment：RESIDUES 1-153	;5'-D(DTDCDTDGDCDCDTDTDTDTDTDT DGPDAP)-3' ; × 1 ;5'-D(DTDTDADGDGDADTDCDCDTDTDC DAPDAP)-3' ; × 1 5'-D(DADADADADGDGDCDADGDAP)-3' × 1 5'-D(DADGDGDADTDCDCDTDADAP)-3' × 1 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；4 MG/ML PROTEIN, 35% METHANOL, 0.1M NACACODYLATE PH 6.5	Resolution 1.80 Å R-free 0.197

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 2VBL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AF5 GROUP I MOBILE INTRON ENDONUCLEASE Deposited 1997-03-21	Different construct Different mutation/modification 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 4–138（135 aa）	Mutation：D56G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；PROTEIN WAS CRYSTALLIZED FROM 23% PEG 6000, 0.1M CITRATE,PH 5.0	Resolution 3.00 Å R-free 0.373
1BP7 GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DNA Deposited 1998-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–153（152 aa） Chain B 2–153（152 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 3.00 Å R-free 0.281
1BP7 GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DNA Deposited 1998-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 2–153（152 aa） Chain D 2–153（152 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 3.00 Å R-free 0.281
1G9Y HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM Deposited 2000-11-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–153（152 aa） Chain B 2–153（152 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；25% PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.05 Å R-free 0.260
1G9Z LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEX WITH MAGNESIUM Deposited 2000-11-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–153（152 aa） Chain B 2–153（152 aa）	Not recorded	MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；30% PEG400, PH 6.5, VAPOR DIFFUSION, HANGING DROP	Resolution 1.80 Å R-free 0.249
1N3E Crystal structure of I-CreI bound to a palindromic DNA sequence I (palindrome of left side of wildtype DNA target sequence) Deposited 2002-10-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–163（163 aa） Chain B 1–163（163 aa）	Not recorded	CA CALCIUM ION × 3 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；25% PEG 400, 20 mM NaCl, 10 mM CaCl2, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.245
1N3E Crystal structure of I-CreI bound to a palindromic DNA sequence I (palindrome of left side of wildtype DNA target sequence) Deposited 2002-10-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain G 1–163（163 aa） Chain H 1–163（163 aa）	Not recorded	CA CALCIUM ION × 3 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；25% PEG 400, 20 mM NaCl, 10 mM CaCl2, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.245
1N3F Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence) Deposited 2002-10-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–163（163 aa） Chain B 1–163（163 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；25% PEG 400, 20 mM NaCl, 10 mM CaCl2, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.228
1N3F Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence) Deposited 2002-10-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain G 1–163（163 aa） Chain H 1–163（163 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；25% PEG 400, 20 mM NaCl, 10 mM CaCl2, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.228
1T9I I-CreI(D20N)/DNA complex Deposited 2004-05-17	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: tetrameric	Chain A 1–163（163 aa） Chain B 1–163（163 aa）	Mutation：D20N Mutation：D20N	CA CALCIUM ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；PEG400, sodium chloride, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP	Resolution 1.60 Å R-free 0.211
1T9J I-CreI(Q47E)/DNA complex Deposited 2004-05-17	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: tetrameric	Chain A 1–163（163 aa） Chain B 1–163（163 aa）	Mutation：Q47E Mutation：Q47E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；PEG 400, sodium chloride, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.00 Å R-free 0.268
1U0C Y33C Mutant of Homing endonuclease I-CreI Deposited 2004-07-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–163（163 aa） Chain B 1–163（163 aa）	Not recorded	MG MAGNESIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.277
1U0D Y33H Mutant of Homing endonuclease I-CreI Deposited 2004-07-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–163（163 aa） Chain B 1–163（163 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.257
2I3P K28R mutant of Homing Endonuclease I-CreI Deposited 2006-08-20	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: tetrameric	Chain A 1–153（153 aa） Chain B 1–153（153 aa）	Mutation：K28R Mutation：K28R	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；PEG 400 28%, pH 6.5, VAPOR DIFFUSION, temperature 298K	Resolution 2.30 Å R-free 0.292
2I3Q Q44V mutant of Homing Endonuclease I-CreI Deposited 2006-08-20	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: tetrameric	Chain A 1–153（153 aa） Chain B 1–153（153 aa）	Mutation：Q44V Mutation：Q44V	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；PEG 400 28%, pH 6.5, VAPOR DIFFUSION, temperature 298K	Resolution 2.30 Å R-free 0.264
2O7M The C-terminal loop of the homing endonuclease I-CreI is essential for DNA binding and cleavage. Identification of a novel site for specificity engineering in the I-CreI scaffold Deposited 2006-12-11	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 1–156（156 aa） Fragment：residues 1-156 Chain B 1–156（156 aa） Fragment：residues 1-156	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.235
2VBJ Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers Deposited 2007-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–153（152 aa） Fragment：RESIDUES 2-153 Chain B 2–153（152 aa） Fragment：RESIDUES 2-153	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；HANGING-DROP DNA-PROTEIN COMPLEX SOLUTION WAS 4 MG/ML. 35% 2-ETHOXYETHANOL IN 0.1M NA-CACODYLATE PH6.5	Resolution 1.95 Å R-free 0.216
2VBN Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers Deposited 2007-09-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–153（153 aa） Fragment：RESIDUES 1-153 Chain B 1–153（153 aa） Fragment：RESIDUES 1-153	Not recorded	MG MAGNESIUM ION × 3 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；4 MG/ML PROTEIN, 20% PEG1000, 0.1M IMIDAZOLE PH 8.0, 0.2 M CAAC2	Resolution 1.90 Å R-free 0.223
2VBO Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers Deposited 2007-09-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–153（153 aa） Fragment：RESIDUES 1-153 Chain B 1–153（153 aa） Fragment：RESIDUES 1-153	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 1.80 Å R-free 0.225
4AAB Crystal structure of the mutant D75N I-CreI in complex with its wild- type target (The four central bases, 2NN region, are composed by GTAC from 5' to 3') Deposited 2011-12-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–153（152 aa） Chain B 2–153（152 aa）	Mutation：YES Mutation：YES	PGO S-1,2-PROPANEDIOL × 5 MG MAGNESIUM ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；30% PROPANEDIOL, 0.1M HEPES PH 7.5, 20% PEG400	Resolution 2.50 Å R-free 0.225
4AAD Crystal structure of the mutant D75N I-CreI in complex with its wild- type target in absence of metal ions at the active site (The four central bases, 2NN region, are composed by GTAC from 5' to 3') Deposited 2011-12-01	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: tetrameric	Chain A 2–153（152 aa） Chain B 2–153（152 aa）	Mutation：YES Mutation：YES	GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；20% PEG300, 0.1M TRIS PH 8.5, 5% PEG8000, 10% GLYCEROL	Resolution 3.10 Å R-free 0.238
4AAE Crystal structure of the mutant D75N I-CreI in complex with an altered target (The four central bases, 2NN region, are composed by AGCG from 5' to 3') Deposited 2011-12-01	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: tetrameric	Chain A 2–154（153 aa） Chain B 2–154（153 aa）	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.5；50% PEG400, 0.1M CHES PH 9.5, 0.2M NACL	Resolution 2.60 Å R-free 0.242
4AAF Crystal structure of the mutant D75N I-CreI in complex with an altered target (The four central bases, 2NN region, are composed by TGCA from 5' to 3') Deposited 2011-12-01	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: tetrameric	Chain A 2–153（152 aa） Chain B 2–153（152 aa）	Mutation：YES Mutation：YES	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；35% METOH, 0.1M SODIUM CACODYLATE PH 6.5,	Resolution 2.50 Å R-free 0.247
4AAG Crystal structure of the mutant D75N I-CreI in complex with its wild- type target in presence of Ca at the active site (The four central bases, 2NN region, are composed by GTAC from 5' to 3') Deposited 2011-12-01	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: tetrameric	Chain A 2–153（152 aa） Chain B 2–153（152 aa）	Mutation：YES Mutation：YES	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；30% PEG400, 0.1M HEPES PH 7.5, 0.1M NACL	Resolution 2.80 Å R-free 0.250
4AQU Crystal structure of I-CreI complexed with its target methylated at position plus 2 (in the b strand) in the presence of calcium Deposited 2012-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–153（152 aa） Fragment：RESIDUES 2-153 Chain B 2–153（152 aa） Fragment：RESIDUES 2-153	Not recorded	CA CALCIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.249
4AQX Crystal structure of I-CreI complexed with its target methylated at position plus 2 (in the b strand) in the presence of magnesium Deposited 2012-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–153（152 aa） Fragment：RESIDUES 2-153 Chain B 2–153（152 aa） Fragment：RESIDUES 2-153	Not recorded	GOL GLYCEROL × 5 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.242
6FB2 Crystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with its target DNA (Haemoglobin beta subunit gene) in the presence of Manganese Deposited 2017-12-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–154（153 aa） Chain B 2–155（154 aa）	Not recorded	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M calcium acetate, 0.1 M sodium acetate pH 4.6-5.4, 33-40% (v/v) 1,2-propanediol	Resolution 2.95 Å R-free 0.235
6FB7 Crystal Structure of the I-CreI Homing Endonuclease D75N variant in complex with its target DNA in the presence of Manganese Deposited 2017-12-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–153（152 aa） Chain B 2–153（152 aa）	Not recorded	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M calcium acetate, 0.1 M sodium acetate pH 4.6-5.4, 33-40% (v/v) 1,2-propanediol	Resolution 2.69 Å R-free 0.211
6FB8 Crystal Structure of the I-CreI Homing Endonuclease D75N variant in complex with an altered version of its target DNA at 5NNN region in the presence of Magnesium Deposited 2017-12-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–153（152 aa） Chain B 2–153（152 aa）	Not recorded	MG MAGNESIUM ION × 4 PGO S-1,2-PROPANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M calcium acetate, 0.1 M sodium acetate pH 4.6-5.4, 33-40% (v/v) 1,2-propanediol	Resolution 2.45 Å R-free 0.224
6FB9 Crystal Structure of the I-CreI Homing Endonuclease D75N variant in complex with an altered version of its target DNA at 5NNN region in the presence of Manganese Deposited 2017-12-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 2–153（152 aa） Chain B 2–153（152 aa）	Not recorded	MN MANGANESE (II) ION × 5 PGO S-1,2-PROPANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M calcium acetate, 0.1 M sodium acetate pH 4.6-5.4, 33-40% (v/v) 1,2-propanediol	Resolution 2.95 Å R-free 0.203

27 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DNE1_CHLRE
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–153； UniProt 1–153 Author chain B； PDBConstruct 1–153； UniProt 1–153

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	2vbl
Deposition date deposition_date	2007-09-14
Structure title title	Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers
Keywords keywords	;UV-INDUCED DNA DAMAGE, CUTTING DNA ENDONUCLEASES, PLASTID, NUCLEASE, HYDROLASE, CHLOROPLAST, ENDONUCLEASE, INTRON HOMING, AMEL3- 4_MAGNESIUM, DOUBLE STRAND BREAK (DSB), HOMING ENDONUCLEASES (HES) ;; HYDROLASE
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	24.80 Å
Radius of gyration Rg (electron density) rg_electron	24.17 Å
Forward intensity I(0) i0	53828300.00
Molecular weight molecular_weight	49490.0 kDa
Excluded volume excluded_volume	58607 Å³
Envelope volume envelope_volume	70241 Å³
Hydration-shell volume shell_volume	25180 Å³
Envelope diameter envelope_diameter	88.1 Å
Shell Rg shell_rg	30.80 Å
Envelope Rg envelope_rg	24.65 Å
Shape Rg shape_rg	24.13 Å
Total Rg total_rg	24.92 Å
Total atoms total_atoms	3431
Residues n_residues	352
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	90.5 Å
Rg (real space) rg_real	25.00 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	5.3830e+07
I(0) uncertainty (real space) i0_real_error	8.3590e+05
Rg (reciprocal space) rg_reciprocal	24.96 Å
I(0) (reciprocal space) i0_reciprocal	53830000.0000
Solution quality estimate total_estimate	0.6528
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.9 Å
Skewness Skewness skewness	0.561
Kurtosis Kurtosis kurtosis	-0.161
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6541000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.596; Stabil: 1.000; Sysdev: 0.338; Positv: 1.000; Valcen: 0.682; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	DNA ENDONUCLEASE I-CREI
Molecular weight formula_weight	17640.3 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3825

MNTKYNKEFLLYLAGFVDGDGSIIAQIEPNASYKFKHRLKLTFKVTQKTQRRWFLDKLVDEIGVGYVRDEGSVSNYILSEIKPLRNFLTQLQPFLKLKQKQANLVLKITEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD

来源 Source

来源生物 organism	CHLAMYDOMONAS REINHARDTII
NCBI Class编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	DNA ENDONUCLEASE I-CREI
Molecular weight formula_weight	17469.2 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MNTKYNKEFLLYLAGFVDADGSIIAQIAPNQSSKFKHRLKLTFQVTQKTQRRWFLDKLVDEIGVGYVRGSGSVSNYILSEIKPLHNFLTQLQPFLKLKQKQANLVLKIIEQLPSAKESPDKFLEVCTWVDQIAALNDSKTRKTTSETVRAVLD

来源 Source

来源生物 organism	CHLAMYDOMONAS REINHARDTII
NCBI Class编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 polymer

Description description	;5'-D(DTDCDTDGDCDCDTDTDTDTDTDT DGPDAP)-3' ;
Molecular weight formula_weight	4227.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

TCTGCCTTTTTTGA

Entity 4 Entity 4 polymer

Description description	;5'-D(DTDTDADGDGDADTDCDCDTDTDC DAPDAP)-3' ;
Molecular weight formula_weight	4254.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

TTAGGATCCTTCAA

Entity 5 Entity 5 polymer

Description description	5'-D(DADADADADGDGDCDADGDAP)-3'
Molecular weight formula_weight	3111.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	S

AAAAGGCAGA

Entity 6 Entity 6 polymer

Description description	5'-D(DADGDGDADTDCDCDTDADAP)-3'
Molecular weight formula_weight	3053.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

AGGATCCTAA

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	394

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2vbla_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.95 — Homing endonuclease-like
Superfamily Superfamily superfamily	d.95.2 — Homing endonucleases
Family Family family	d.95.2.1 — Group I mobile intron endonuclease

Domain ID domain_id	d2vblb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.95 — Homing endonuclease-like
Superfamily Superfamily superfamily	d.95.2 — Homing endonucleases
Family Family family	d.95.2.1 — Group I mobile intron endonuclease

CATH v4.4 (2 domains)

Domain ID domain_id	2vblA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	28 — Endonuclease I-creI
Homologous superfamily homologous superfamily	10 — Homing endonucleases

Domain ID domain_id	2vblB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	28 — Endonuclease I-creI
Homologous superfamily homologous superfamily	10 — Homing endonucleases

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8. Citations (1)

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Unit-cell length a length_a	44.612 Å
Unit-cell length b length_b	69.209 Å
Unit-cell length c length_c	88.671 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.46 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	32.920 Å
R factor r_factor	0.1490
R_work r_work	0.1470
R_free r_free	0.1970

fit	/app/data/saxs_computation/vb/2vbl/2vbl.fit
pddf	/app/data/pr_computation/vb/2vbl/2vbl.pr.out
profile	/app/data/saxs_computation/vb/2vbl/2vbl.dat

Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers

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

DNA ENDONUCLEASE I-CREI

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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)