SAXSdb — 5gox

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

DNA repair protein RAD50

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 585–766 Chain B； UniProt 585–766	Fragment：UNP residues 585-766 Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.7；291 K；28 - 30% PEG 600, 0.1 M bis-tris propane, 3% 1, 6-hexanediol, 5 mM DTT	Resolution 2.40 Å R-free 0.271

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 5GOX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9Q9H Cryo-EM structure of human Mre11-Rad50 complex bound to DNA Deposited 2025-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 1–1312（1312 aa） Chain B 1–1312（1312 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 MN MANGANESE (II) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25mM Hepes-NaOH, pH 7.5, 150 mM NaCl, 1 mM DTT, 1 mM ATP, 1mM BeF3, 5 mM MgCl2, 1 mM MnCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.11 Å
9Q9I Cryo-EM structure of human Mre11-Rad50-Nbs1 complex bound to DNA Deposited 2025-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain A 1–1312（1312 aa） Chain B 1–1312（1312 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25mM Hepes-NaOH, pH 7.5, 150 mM NaCl, 1 mM DTT, 1 mM ATP, 1mM BeF3, 5 mM MgCl2, 1 mM MnCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.79 Å
9Q9J Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric factor TRF2 fragment (438-542) Deposited 2025-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–1312（1312 aa） Chain B 1–1312（1312 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 MN MANGANESE (II) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25mM Hepes-NaOH, pH 7.5, 150 mM NaCl, 1 mM DTT, 1 mM ATP, 1mM BeF3, 5 mM MgCl2, 1 mM MnCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.71 Å
9Q9K Cryo-EM structure of human Mre11-Rad50 (MR) complex bound to DNA and telomeric factor TRF2 fragment (438-542) Deposited 2025-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–1312（1312 aa） Chain B 1–1312（1312 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 MN MANGANESE (II) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25mM Hepes-NaOH, pH 7.5, 150 mM NaCl, 1 mM DTT, 1 mM ATP, 1mM BeF3, 5 mM MgCl2, 1 mM MnCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.59 Å
9Q9M Cryo-EM structure of human Mre11-Rad50-Nbs1 (MRN) complex bound to DNA and telomeric factor TRF2 Deposited 2025-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–1312（1312 aa） Chain B 1–1312（1312 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 MN MANGANESE (II) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25mM Hepes-NaOH, pH 7.5, 150 mM NaCl, 1 mM DTT, 1 mM ATP, 1mM BeF3, 5 mM MgCl2, 1 mM MnCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å

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

View Construct and Data Evidence

UniProt name	RAD50_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–186； UniProt 585–766 Author chain B； PDBConstruct 5–186； UniProt 585–766

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	5gox
Deposition date deposition_date	2016-07-30
Structure title title	Eukaryotic Rad50 Functions as A Rod-shaped Dimer
Keywords keywords	DNA repair, HYDROLASE; 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	35.84 Å
Radius of gyration Rg (electron density) rg_electron	36.76 Å
Forward intensity I(0) i0	32954800.00
Molecular weight molecular_weight	42847.0 kDa
Excluded volume excluded_volume	52771 Å³
Envelope volume envelope_volume	78352 Å³
Hydration-shell volume shell_volume	21391 Å³
Envelope diameter envelope_diameter	137.4 Å
Shell Rg shell_rg	34.55 Å
Envelope Rg envelope_rg	38.06 Å
Shape Rg shape_rg	36.79 Å
Total Rg total_rg	36.45 Å
Total atoms total_atoms	2971
Residues n_residues	356
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	140.3 Å
Rg (real space) rg_real	36.66 Å
Rg uncertainty (real space) rg_real_error	1.91 Å
I(0) (real space) i0_real	3.2950e+07
I(0) uncertainty (real space) i0_real_error	6.4860e+05
Rg (reciprocal space) rg_reciprocal	36.15 Å
I(0) (reciprocal space) i0_reciprocal	32940000.0000
Solution quality estimate total_estimate	0.6853
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.5 Å
Skewness Skewness skewness	0.722
Kurtosis Kurtosis kurtosis	-0.106
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2229000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.324; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.072; Smooth: 0.862

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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 repair protein RAD50
Molecular weight formula_weight	21876.2 kDa
EC 编号 ec_number	3.6.-.-
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	2980

GSHMKEINQTRDRLAKLNKELASSEQNKNHINNELKRKEEQLSSYEDKLFDVCGSQDFESDLDRLKEEIEKSSKQRAMLAGATAVYSQFITQLTDENQSCCPVCQRVFQTEAELQEVISDLQSKLRLAPDKLKSTESELKKKEKRRDEMLGLVPMRQSIIDLKEKEIPELRNKLQNVNRDIQRLKN

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

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	9

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8. Citations (1)

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Unit-cell length a length_a	42.180 Å
Unit-cell length b length_b	61.972 Å
Unit-cell length c length_c	81.540 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.75 °
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	2.405 Å
Low-resolution limit resolution_low	28.221 Å
R factor r_factor	0.2164
R_work r_work	0.2132
R_free r_free	0.2709

fit	/app/data/saxs_computation/go/5gox/5gox.fit
pddf	/app/data/pr_computation/go/5gox/5gox.pr.out
profile	/app/data/saxs_computation/go/5gox/5gox.dat

Eukaryotic Rad50 Functions as A Rod-shaped Dimer

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

DNA repair protein RAD50

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