SAXSdb — 6d0l

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

Tudor-interacting repair regulator protein

Homo sapiens

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 6–211 Chain B； UniProt 6–211	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；0.06 M citric acid, 0.04 M Bis-Tris-Propane, pH 4.1, 16% PEG 3,350; Cryoprotection in 25% PEG 3,350	Resolution 1.97 Å R-free 0.209

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 6D0L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3KVH Crystal structure of human protein syndesmos (NUDT16-like protein) Deposited 2009-11-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 6–211（206 aa）	Not recorded	GOL GLYCEROL × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M hepes pH 7.5, 20%w/v jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.70 Å R-free 0.217
5ZCJ Crystal structure of complex Deposited 2018-02-17	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 6–211（206 aa） Chain B 6–211（206 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.7 M Ammonium tartrate, 0.1 M Sodium acetate pH 4.6	Resolution 2.00 Å R-free 0.219
6CO1 Structure of human TIRR in complex with 53BP1 Tudor domains Deposited 2018-03-10	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 6–211（206 aa） Chain B 6–211（206 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M MES, pH 5.5, 0.2 M calcium acetate, 7% isopropanol	Resolution 2.18 Å R-free 0.203
6CO1 Structure of human TIRR in complex with 53BP1 Tudor domains Deposited 2018-03-10	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 6–211（206 aa） Chain D 6–211（206 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M MES, pH 5.5, 0.2 M calcium acetate, 7% isopropanol	Resolution 2.18 Å R-free 0.203
8U3S Structure of human TIRR in complex with VHH4 nanobody Deposited 2023-09-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 6–211（206 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；Crystals were produced by the hanging-drop vapor diffusion method by mixing 2 microliters of the protein (in 10 mM HEPES, 50 mM NaCl, 2 mM TCEP, pH 7.5) and 2 microliters of the reservoir solution made up of 8% Tacsimate, pH 5, and 20% PEG 3,350	Resolution 1.85 Å R-free 0.271

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TIRR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–207； UniProt 6–211 Author chain B； PDBConstruct 2–207； UniProt 6–211

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	6d0l
Deposition date deposition_date	2018-04-10
Structure title title	Structure of human TIRR
Keywords keywords	Protein binding, RNA binding, NUDT16L1, 53BP1, DNA damage response, DNA double-strand break repair; PROTEIN BINDING
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	22.60 Å
Radius of gyration Rg (electron density) rg_electron	21.41 Å
Forward intensity I(0) i0	30329600.00
Molecular weight molecular_weight	43308.0 kDa
Excluded volume excluded_volume	54756 Å³
Envelope volume envelope_volume	65125 Å³
Hydration-shell volume shell_volume	25182 Å³
Envelope diameter envelope_diameter	82.9 Å
Shell Rg shell_rg	28.67 Å
Envelope Rg envelope_rg	21.67 Å
Shape Rg shape_rg	21.43 Å
Total Rg total_rg	22.29 Å
Total atoms total_atoms	6113
Residues n_residues	396
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	79.4 Å
Rg (real space) rg_real	22.54 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	3.0330e+07
I(0) uncertainty (real space) i0_real_error	4.1220e+05
Rg (reciprocal space) rg_reciprocal	22.55 Å
I(0) (reciprocal space) i0_reciprocal	30330000.0000
Solution quality estimate total_estimate	0.6499
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.336
Kurtosis Kurtosis kurtosis	-0.056
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8337000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.688; Stabil: 1.000; Sysdev: 0.130; Positv: 1.000; Valcen: 0.997; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6d0la_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.0 — automated matches

Domain ID domain_id	d6d0lb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	6d0lA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

Domain ID domain_id	6d0lB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

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8. Citations (1)

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Unit-cell length a length_a	41.890 Å
Unit-cell length b length_b	46.360 Å
Unit-cell length c length_c	48.800 Å
Unit-cell angle α angle_alpha	92.31 °
Unit-cell angle β angle_beta	108.07 °
Unit-cell angle γ angle_gamma	105.75 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.970 Å
Low-resolution limit resolution_low	38.000 Å
R factor r_factor	0.1760
R_work r_work	0.1742
R_free r_free	0.2091

Description description	Tudor-interacting repair regulator protein
Molecular weight formula_weight	23038.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6760

Structure of human TIRR

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

Tudor-interacting repair regulator protein

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 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)

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	351

fit	/app/data/saxs_computation/d0/6d0l/6d0l.fit
pddf	/app/data/pr_computation/d0/6d0l/6d0l.pr.out
profile	/app/data/saxs_computation/d0/6d0l/6d0l.dat