SAXSdb — 3sm4

▼

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

Exonuclease

Enterobacteria phage lambda

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 × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain A； UniProt 1–226 Chain B； UniProt 1–226 Chain C； UniProt 1–226	Mutation：K131A	5'-D(TPCPGPGPTPAPCPAPGPTPAPG)-3' × 1 5'-D(PAPGPCPTPAPCPTPGPTPAPCPCPGPA)-3' × 1 PO4 PHOSPHATE ION × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；19% PEG3350, 0.2 M sodium bromide, 5 mM magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.88 Å R-free 0.186

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 3SM4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AVQ TOROIDAL STRUCTURE OF LAMBDA EXONUCLEASE DETERMINED AT 2.4 ANGSTROMS Deposited 1997-09-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–226（226 aa） Chain B 1–226（226 aa） Chain C 1–226（226 aa）	Mutation：20 AMINO ACID N-TERMINAL HIS-TAG Mutation：20 AMINO ACID N-TERMINAL HIS-TAG Mutation：20 AMINO ACID N-TERMINAL HIS-TAG	PO4 PHOSPHATE ION × 3 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.7；277 K；PROTEIN WAS CRYSTALLIZED FROM 1.2 M NH2SO4, 0.2 M NACL 0.1 M NAACETATE PH 4.7, AT 4 DEGREES CELSIUS., temperature 277K	Resolution 2.40 Å
3SLP Crystal Structure of Lambda Exonuclease in Complex with a 12 BP Symmetric DNA Duplex Deposited 2011-06-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric	Chain A 1–226（226 aa） Chain B 1–226（226 aa） Chain C 1–226（226 aa）	Not recorded	CA CALCIUM ION × 3 PO4 PHOSPHATE ION × 3 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；295 K；22% PEG3350, 0.3 M sodium acetate, 0.1 M Tris, 5 mM calcium chloride, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.30 Å R-free 0.281
4WUZ Crystal structure of lambda exonuclease in complex with DNA and Ca2+ Deposited 2014-11-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 3 PDB declaration: pentameric	Chain A 1–226（226 aa） Chain B 1–226（226 aa） Chain C 1–226（226 aa）	Not recorded	CA CALCIUM ION × 3 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；295 K；23.4% PEG 3350, 0.3M sodium acetate, 0.1 M Tris	Resolution 2.38 Å R-free 0.319
6M9K Crystal structure of lambda exonuclease in complex with the Red beta C-terminal domain Deposited 2018-08-23	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–226（226 aa） Chain B 1–226（226 aa） Chain C 1–226（226 aa）	Not recorded	SO4 SULFATE ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；PEG3350, LISO4, BIS-TRIS	Resolution 2.30 Å R-free 0.254

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EXO_LAMBD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–229； UniProt 1–226 Author chain B； PDBConstruct 4–229； UniProt 1–226 Author chain C； PDBConstruct 4–229； UniProt 1–226

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3sm4
Deposition date deposition_date	2011-06-27
Structure title title	Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium
Keywords keywords	;homologous recombination, DNA repair, recombineering, single-strand annealing, Type II Restriction Endonuclease Fold, 5'-3' dsDNA exonuclease, HYDROLASE-DNA complex ;; HYDROLASE/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	29.26 Å
Radius of gyration Rg (electron density) rg_electron	28.81 Å
Forward intensity I(0) i0	137702000.00
Molecular weight molecular_weight	86206.0 kDa
Excluded volume excluded_volume	105060 Å³
Envelope volume envelope_volume	136700 Å³
Hydration-shell volume shell_volume	39142 Å³
Envelope diameter envelope_diameter	90.6 Å
Shell Rg shell_rg	36.49 Å
Envelope Rg envelope_rg	28.12 Å
Shape Rg shape_rg	28.82 Å
Total Rg total_rg	29.49 Å
Total atoms total_atoms	6023
Residues n_residues	708
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

▼

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

Maximum dimension Dmax dmax	88.5 Å
Rg (real space) rg_real	29.13 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	1.3770e+08
I(0) uncertainty (real space) i0_real_error	2.2540e+06
Rg (reciprocal space) rg_reciprocal	29.19 Å
I(0) (reciprocal space) i0_reciprocal	137700000.0000
Solution quality estimate total_estimate	0.9122
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.150
Kurtosis Kurtosis kurtosis	-0.593
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18010000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.960

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Exonuclease
Molecular weight formula_weight	26164.8 kDa
EC 编号 ec_number	3.1.11.3
Mutation mutation	K131A
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6607

GSHMTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELACPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR

来源 Source

来源生物 organism	Enterobacteria phage lambda
NCBI Class编号 ncbi_taxonomy_id	10710
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(TPCPGPGPTPAPCPAPGPTPAPG)-3'
Molecular weight formula_weight	3702.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TCGGTACAGTAG

Entity 3 Entity 3 polymer

Description description	5'-D(PAPGPCPTPAPCPTPGPTPAPCPCPGPA)-3'
Molecular weight formula_weight	4264.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

AGCTACTGTACCGA

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	584

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3sm4a_
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.52.1.13 — lambda exonuclease

Domain ID domain_id	d3sm4b1
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.52.1.13 — lambda exonuclease

Domain ID domain_id	d3sm4b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3sm4c1
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.52.1.13 — lambda exonuclease

Domain ID domain_id	d3sm4c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	3sm4A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	320 — Lambda Exonuclease; Chain A
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3sm4B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	320 — Lambda Exonuclease; Chain A
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3sm4C00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	320 — Lambda Exonuclease; Chain A
Homologous superfamily homologous superfamily	10 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	78.391 Å
Unit-cell length b length_b	78.391 Å
Unit-cell length c length_c	247.534 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	18

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	67.890 Å
R factor r_factor	0.1611
R_work r_work	0.1598
R_free r_free	0.1858

fit	/app/data/saxs_computation/sm/3sm4/3sm4.fit
pddf	/app/data/pr_computation/sm/3sm4/3sm4.pr.out
profile	/app/data/saxs_computation/sm/3sm4/3sm4.dat

Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium

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

Exonuclease

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)