SAXSdb — 7ogg

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

;Non-structural maintenance of chromosome element 5,Non-structural maintenance of chromosome element 5,Non-structural maintenance of chromosome element 5 ;

Saccharomyces cerevisiae A364A

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain R； UniProt 1–556	Non-standard monomer：Yes (specific site not provided by mmCIF)	DNA repair protein KRE29,DNA repair protein KRE29,DNA repair protein KRE29 × 1 （P40026）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；2% (w/v) PEG 3350, 8% (v/v) 0.3 M Sodium malonate pH 7.5	Resolution 3.29 Å R-free 0.317

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 7OGG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7LTO Nse5-6 complex Deposited 2021-02-19	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–556（556 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7SDE Cryo-EM structure of Nse5/6 heterodimer Deposited 2021-09-29	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–556（556 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7YQH Cryo-EM structure of 8-subunit Smc5/6 Deposited 2022-08-07	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–556（556 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.60 Å
8HQS Cryo-EM structure of 8-subunit Smc5/6 head region Deposited 2022-12-14	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain E 1–556（556 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8I4W Cryo-EM structure of 5-subunit Smc5/6 head region Deposited 2023-01-21	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–556（556 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.01 Å
8I4X Cryo-EM structure of 5-subunit Smc5/6 Deposited 2023-01-21	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–556（556 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.50 Å
8T8E cryoEM structure of Smc5/6 5mer Deposited 2023-06-22	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–556（556 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM Hepes, pH 7.5, 250 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8T8F Smc5/6 8mer Deposited 2023-06-22	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–556（556 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM Hepes, pH 7.5, 250 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NSE5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain R； PDBConstruct 1–556； UniProt 1–556

DNA repair protein KRE29,DNA repair protein KRE29,DNA repair protein KRE29

Saccharomyces cerevisiae A364A

UniProt P40026

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain Q； UniProt 177–464	Non-standard monomer：Yes (specific site not provided by mmCIF)	;Non-structural maintenance of chromosome element 5,Non-structural maintenance of chromosome element 5,Non-structural maintenance of chromosome element 5 ; × 1 （Q03718）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；2% (w/v) PEG 3350, 8% (v/v) 0.3 M Sodium malonate pH 7.5	Resolution 3.29 Å R-free 0.317

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 7OGG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6J0W Crystal Structure of Yeast Rtt107 and Nse6 Deposited 2018-12-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 13–41（29 aa） Fragment：Rtt107 interacting motif	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；277 K；22% PEG 3350, 0.1M Bis-Tris pH 6.0, 0.2M ammonium acetate	Resolution 2.40 Å R-free 0.271
6J0W Crystal Structure of Yeast Rtt107 and Nse6 Deposited 2018-12-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 13–41（29 aa） Fragment：Rtt107 interacting motif	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；277 K；22% PEG 3350, 0.1M Bis-Tris pH 6.0, 0.2M ammonium acetate	Resolution 2.40 Å R-free 0.271
7LTO Nse5-6 complex Deposited 2021-02-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–464（464 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7SDE Cryo-EM structure of Nse5/6 heterodimer Deposited 2021-09-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–464（464 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7YQH Cryo-EM structure of 8-subunit Smc5/6 Deposited 2022-08-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–464（464 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.60 Å
8HQS Cryo-EM structure of 8-subunit Smc5/6 head region Deposited 2022-12-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 1–464（464 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8I4V Cryo-EM structure of 5-subunit Smc5/6 arm region Deposited 2023-01-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 87–150（64 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.97 Å
8I4W Cryo-EM structure of 5-subunit Smc5/6 head region Deposited 2023-01-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–464（464 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.01 Å
8I4X Cryo-EM structure of 5-subunit Smc5/6 Deposited 2023-01-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 87–464（378 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.50 Å
8T8E cryoEM structure of Smc5/6 5mer Deposited 2023-06-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–464（464 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM Hepes, pH 7.5, 250 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8T8F Smc5/6 8mer Deposited 2023-06-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–464（464 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM Hepes, pH 7.5, 250 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
8WJO Cryo-EM structure of 8-subunit Smc5/6 arm region Deposited 2023-09-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–464（464 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.04 Å

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KRE29_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain Q； PDBConstruct 6–293； UniProt 177–464

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	7ogg
Deposition date deposition_date	2021-05-06
Structure title title	Nse5/6 complex
Keywords keywords	NSe5/6, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	28.06 Å
Radius of gyration Rg (electron density) rg_electron	26.59 Å
Forward intensity I(0) i0	77117800.00
Molecular weight molecular_weight	69395.0 kDa
Excluded volume excluded_volume	86817 Å³
Envelope volume envelope_volume	116740 Å³
Hydration-shell volume shell_volume	35628 Å³
Envelope diameter envelope_diameter	96.1 Å
Shell Rg shell_rg	34.65 Å
Envelope Rg envelope_rg	27.33 Å
Shape Rg shape_rg	26.65 Å
Total Rg total_rg	27.25 Å
Total atoms total_atoms	4880
Residues n_residues	655
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	91.5 Å
Rg (real space) rg_real	27.98 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	7.7120e+07
I(0) uncertainty (real space) i0_real_error	1.0920e+06
Rg (reciprocal space) rg_reciprocal	28.01 Å
I(0) (reciprocal space) i0_reciprocal	77120000.0000
Solution quality estimate total_estimate	0.6895
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.3 Å
Skewness Skewness skewness	0.324
Kurtosis Kurtosis kurtosis	-0.228
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22530000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.852; Stabil: 0.999; Sysdev: 0.177; Positv: 1.000; Valcen: 1.000; Smooth: 0.874

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	;Non-structural maintenance of chromosome element 5,Non-structural maintenance of chromosome element 5,Non-structural maintenance of chromosome element 5 ;
Molecular weight formula_weight	68795.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R
Atom count atom_count	4888

MDGALINSVLYVSPRNGAHYFVELTEKHLLAFEMLNSMCLLENYDHVLLFLECQFGKSHNLAVIPFDIILVLFTLSTLSEYYKEPILRANDPYNTSRETLSRRALKLLQKYLAILKEFDSEQYNLYDLELLRCQFFLAIDTLTPKKQKWGFDRFRRTKSESGVTYRQNASVDPELDQAKTFKNPYRSYISCLEQRNTILGNRLLNLKLNEPGEFINMILWTLSNSLQESTPLFLSSHEIWMPLLEILIDLFSCRQDYFIQHEVAQNVSKSLFVQRLSESPLAVFFESLNTRNFANRFSEYVFLNCDYKLPSDNYATPVHPVYNGENTIVDTYIPTIKCSPLYKSQKSLALRRKLIGSCFKLLLRVPDGHRLITPRIVADDVIQGISRTLASFNDILQFKKFFMTENLSQESYFIPLLAEGTLSEILKDTQECVVILTLVENLSDGVSFCNEVIGLVKSKCFAFTEQCSQASYEEAVLNIEKCDVCLLVLLRYLLHLIGTEAILDAKEQLEMLHAIEKNDSGRRQWAKALNLGNDPPLLYPIVSQMFGVHDKSVIIEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

来源 Source

来源生物 organism	Saccharomyces cerevisiae A364A
NCBI Class编号 ncbi_taxonomy_id	765312
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	DNA repair protein KRE29,DNA repair protein KRE29,DNA repair protein KRE29
Molecular weight formula_weight	36332.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

GPAAMSGSIPEIYLDVVTKETISDKYKDWHFISKNCHYEQLMDLEMKDTAYSFLFGSSRSQGKVPEFVHLKCPSITNLLVLFGVNQEKCNSLKINYEKKENSRYDNLCTIFPVNKMLKFLMYFYSDDDNDDVREFFLKAFICLILDRKVFNAMESDHRLCFKVLELFNEAHFINSYFEIVDKNDFFLHYRLLQIFPHLQSALLRRRFSEKQGRTETIQQNIIKEFNEFFDCKNYKNLLYFILTMYGSKFIPFGPKCQVTEYFKDCILDISNETTNDVEISILKGILNLFSKIRGXXXXXXXXXXXXXX

来源 Source

来源生物 organism	Saccharomyces cerevisiae A364A
NCBI Class编号 ncbi_taxonomy_id	765312
宿主生物 host_organism	Escherichia coli BL21

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8. Citations (1)

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Unit-cell length a length_a	99.116 Å
Unit-cell length b length_b	147.368 Å
Unit-cell length c length_c	74.444 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.290 Å
Low-resolution limit resolution_low	19.850 Å
R factor r_factor	0.2989
R_work r_work	0.2970
R_free r_free	0.3167

fit	/app/data/saxs_computation/og/7ogg/7ogg.fit
pddf	/app/data/pr_computation/og/7ogg/7ogg.pr.out
profile	/app/data/saxs_computation/og/7ogg/7ogg.dat

Nse5/6 complex

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

;Non-structural maintenance of chromosome element 5,Non-structural maintenance of chromosome element 5,Non-structural maintenance of chromosome element 5 ;

State in the Current Structure

Other States of the Same Protein in the Database

DNA repair protein KRE29,DNA repair protein KRE29,DNA repair protein KRE29

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 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)