SAXSdb — 1odg

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

DNA MISMATCH ENDONUCLEASE

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 Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 22–155	Not recorded	5'-D(TPAPGPGPCP5CMTPGPGPAPTPCP)-3' × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；25 MM HEPES PH7.0, 75 MM NACL, 15% PEG 8000, 50 MM SODIUM CACODYLATE PH 6.5, 75 MM AMMONIUM SULPHATE AND 10% GLYCEROL PROTEIN 2.5 MG/ML	Resolution 2.80 Å R-free 0.356

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 1ODG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CW0 CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DNA Deposited 1999-08-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–155（155 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；pH 5.60, VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.230
1VSR VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE FROM ESCHERICHIA COLI Deposited 1999-02-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–156（136 aa） Fragment：FRAGMENT	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；CRYSTALLIZATION CONDITIONS: ROOM TEMPERATURE BATCH, 75 MM SODIUM PHOSPHATE PH 6.5, 150 MM NACL, 2 MM DTT, 10% PEG 4K	Resolution 1.80 Å R-free 0.216

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VSR_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–134； UniProt 22–155

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	1odg
Deposition date deposition_date	2003-02-19
Structure title title	Very-short-patch DNA repair endonuclease bound to its reaction product site
Keywords keywords	HYDROLASE, DNA REPAIR, ENDONUCLEASE, VERY SHORT PATCH REPAIR, DNA REPAI HYDROLASE, NUCLEASE, ZINC, METAL-BINDING; 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	18.85 Å
Radius of gyration Rg (electron density) rg_electron	17.72 Å
Forward intensity I(0) i0	14085600.00
Molecular weight molecular_weight	23065.0 kDa
Excluded volume excluded_volume	26613 Å³
Envelope volume envelope_volume	33991 Å³
Hydration-shell volume shell_volume	16540 Å³
Envelope diameter envelope_diameter	60.4 Å
Shell Rg shell_rg	23.19 Å
Envelope Rg envelope_rg	17.66 Å
Shape Rg shape_rg	17.66 Å
Total Rg total_rg	18.58 Å
Total atoms total_atoms	1591
Residues n_residues	156
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	59.4 Å
Rg (real space) rg_real	18.76 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	1.4090e+07
I(0) uncertainty (real space) i0_real_error	1.7610e+05
Rg (reciprocal space) rg_reciprocal	18.77 Å
I(0) (reciprocal space) i0_reciprocal	14090000.0000
Solution quality estimate total_estimate	0.9052
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.1 Å
Skewness Skewness skewness	0.156
Kurtosis Kurtosis kurtosis	-0.500
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1531000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DNA MISMATCH ENDONUCLEASE
Molecular weight formula_weight	15568.8 kDa
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	1672

AIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPATRTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGEGASAQIDTQGIHLLA

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 2 Entity 2 polymer

Description description	5'-D(TPAPGPGPCP5CMTPGPGPAPTPCP)-3'
Molecular weight formula_weight	3692.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,W

TAGGCCTGGATC

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1odga_
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.52.1.15 — Very short patch repair (VSR) endonuclease

CATH v4.4 (1 domains)

Domain ID domain_id	1odgA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	960 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — VSR Endonuclease

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8. Citations (1)

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Unit-cell length a length_a	102.805 Å
Unit-cell length b length_b	102.805 Å
Unit-cell length c length_c	64.290 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	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	24.700 Å
R factor r_factor	0.2873
R_work r_work	0.2873
R_free r_free	0.3561

fit	/app/data/saxs_computation/od/1odg/1odg.fit
pddf	/app/data/pr_computation/od/1odg/1odg.pr.out
profile	/app/data/saxs_computation/od/1odg/1odg.dat

Very-short-patch DNA repair endonuclease bound to its reaction product site

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

DNA MISMATCH 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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 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)