SAXSdb — 1d3y

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer 蛋白 2 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：DNA TOPOISOMERASE VI A SUBUNIT × 2 缺少 UniProt 身份时不显示参考序列区间	Entity 1Fragment：DNA BINDING CORE Entity 1Mutation：DELETED NONCONSERVED N-TERMINAL RESIDUES 1-69	NA SODIUM ION × 2 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；PEG 8000, MPD, NA-CACODYLATE, MGCL2, NACL, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.242

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	1d3y
Deposition date deposition_date	1999-10-01
Structure title title	STRUCTURE OF THE DNA TOPOISOMERASE VI A SUBUNIT
Keywords keywords	TOPOISOMERASE VI, DNA BINDING PROTEIN, SPO11 HOMOLOG, ISOMERASE; ISOMERASE
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	25.77 Å
Radius of gyration Rg (electron density) rg_electron	24.68 Å
Forward intensity I(0) i0	67738600.00
Molecular weight molecular_weight	65967.0 kDa
Excluded volume excluded_volume	83227 Å³
Envelope volume envelope_volume	99008 Å³
Hydration-shell volume shell_volume	32129 Å³
Envelope diameter envelope_diameter	80.1 Å
Shell Rg shell_rg	33.13 Å
Envelope Rg envelope_rg	24.63 Å
Shape Rg shape_rg	24.67 Å
Total Rg total_rg	25.60 Å
Total atoms total_atoms	4653
Residues n_residues	579
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	79.2 Å
Rg (real space) rg_real	25.60 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	6.7740e+07
I(0) uncertainty (real space) i0_real_error	8.5300e+05
Rg (reciprocal space) rg_reciprocal	25.66 Å
I(0) (reciprocal space) i0_reciprocal	67740000.0000
Solution quality estimate total_estimate	0.9058
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.5 Å
Skewness Skewness skewness	0.074
Kurtosis Kurtosis kurtosis	-0.578
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31560000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.990

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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 TOPOISOMERASE VI A SUBUNIT
Molecular weight formula_weight	34098.8 kDa
EC 编号 ec_number	5.99.1.3
Mutation mutation	DELETED NONCONSERVED N-TERMINAL RESIDUES 1-69
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4979

TVNQAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASNNVIEDLEAALGVLREHLGFIPEEDGSSVVGPLKIIEETPEGELVVDCTKLGTGAYNIPNDVTKLNLETDADFILAIETSGMFARLNAERFWDKHNCILVSLKGVPARATRRFIKRLHEEHDLPVLVFTDGDPYGYLNIYRTLKVGSGKAIHLADKLSIPAARLIGVTPQDIIDYDLPTHPLKEQDIKRIKDGLKNDDFVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIKDESTWLP

来源 Source

来源生物 organism	Methanocaldococcus jannaschii
NCBI Class编号 ncbi_taxonomy_id	2190
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	326

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d3ya_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.12 — DNA topoisomerase IV, alpha subunit
Superfamily Superfamily superfamily	e.12.1 — DNA topoisomerase IV, alpha subunit
Family Family family	e.12.1.1 — DNA topoisomerase IV, alpha subunit

Domain ID domain_id	d1d3yb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.12 — DNA topoisomerase IV, alpha subunit
Superfamily Superfamily superfamily	e.12.1 — DNA topoisomerase IV, alpha subunit
Family Family family	e.12.1.1 — DNA topoisomerase IV, alpha subunit

CATH v4.4 (4 domains)

Domain ID domain_id	1d3yA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1d3yA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1d3yB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1d3yB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	66.510 Å
Unit-cell length b length_b	59.040 Å
Unit-cell length c length_c	87.260 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1970
R_free r_free	0.2420

fit	/app/data/saxs_computation/d3/1d3y/1d3y.fit
pddf	/app/data/pr_computation/d3/1d3y/1d3y.pr.out
profile	/app/data/saxs_computation/d3/1d3y/1d3y.dat

STRUCTURE OF THE DNA TOPOISOMERASE VI A SUBUNIT

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

Assembly Composition of the Current Entry

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