SAXSdb — 1avq

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

LAMBDA 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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–226 Chain B； UniProt 1–226 Chain C； UniProt 1–226	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

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 1AVQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3SLP Crystal Structure of Lambda Exonuclease in Complex with a 12 BP Symmetric DNA Duplex Deposited 2011-06-24	Different mutation/modification Different oligomeric state 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
3SM4 Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium Deposited 2011-06-27	Different mutation/modification Different oligomeric state 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）	Mutation：K131A Mutation：K131A Mutation：K131A	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
4WUZ Crystal structure of lambda exonuclease in complex with DNA and Ca2+ Deposited 2014-11-04	Different mutation/modification Different oligomeric state 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 3–228； UniProt 1–226 Author chain B； PDBConstruct 3–228； UniProt 1–226 Author chain C； PDBConstruct 3–228； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1avq
Deposition date deposition_date	1997-09-18
Structure title title	TOROIDAL STRUCTURE OF LAMBDA EXONUCLEASE DETERMINED AT 2.4 ANGSTROMS
Keywords keywords	;DEOXYRIBONUCLEASE, DNA RECOMBINATION AND REPAIR, 5'-3' EXONUCLEASE ;; DEOXYRIBONUCLEASE
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	30.87 Å
Radius of gyration Rg (electron density) rg_electron	29.80 Å
Forward intensity I(0) i0	102565000.00
Molecular weight molecular_weight	78532.0 kDa
Excluded volume excluded_volume	97774 Å³
Envelope volume envelope_volume	130200 Å³
Hydration-shell volume shell_volume	36352 Å³
Envelope diameter envelope_diameter	90.1 Å
Shell Rg shell_rg	37.36 Å
Envelope Rg envelope_rg	28.52 Å
Shape Rg shape_rg	29.79 Å
Total Rg total_rg	30.59 Å
Total atoms total_atoms	5517
Residues n_residues	681
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	91.0 Å
Rg (real space) rg_real	30.68 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	1.0260e+08
I(0) uncertainty (real space) i0_real_error	1.5540e+06
Rg (reciprocal space) rg_reciprocal	30.77 Å
I(0) (reciprocal space) i0_reciprocal	102600000.0000
Solution quality estimate total_estimate	0.9137
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	46.4 Å
Skewness Skewness skewness	-0.004
Kurtosis Kurtosis kurtosis	-0.792
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22830000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.964

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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	LAMBDA EXONUCLEASE
Molecular weight formula_weight	26165.8 kDa
EC 编号 ec_number	3.1.11.3
Mutation mutation	20 AMINO ACID N-TERMINAL HIS-TAG
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	5933

SHMTPDIILQRTGIDVRAVEQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDMKMSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTESPIIYRDESMRTACSPDGLCSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKNAWYFANYDPRMKREGLHYVVIERDEKYMASFDEIVPEFIEKMDEALAEIGFVFGEQWR

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 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	416

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1avqa_
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	d1avqb_
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	d1avqc_
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

CATH v4.4 (3 domains)

Domain ID domain_id	1avqA00
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	1avqB00
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	1avqC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	320 — Lambda Exonuclease; Chain A
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	156.700 Å
Unit-cell length b length_b	156.700 Å
Unit-cell length c length_c	131.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.1980
R_free r_free	—

fit	/app/data/saxs_computation/av/1avq/1avq.fit
pddf	/app/data/pr_computation/av/1avq/1avq.pr.out
profile	/app/data/saxs_computation/av/1avq/1avq.dat

TOROIDAL STRUCTURE OF LAMBDA EXONUCLEASE DETERMINED AT 2.4 ANGSTROMS

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

LAMBDA 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