SAXSdb — 1m2n

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

Silent Information Regulator 2

Archaeoglobus fulgidus

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 1–245 Chain B； UniProt 1–245	Mutation：D102G, F159A, R170A	ZN ZINC ION × 2 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 7；291 K；PEG 8000, HEPES, pH 7.0, EVAPORATION, temperature 291K	Resolution 2.60 Å R-free 0.308

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 1M2N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ICI CRYSTAL STRUCTURE OF A SIR2 HOMOLOG-NAD COMPLEX Deposited 2001-04-01	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 1–245（245 aa） Chain B 1–245（245 aa）	Not recorded	ZN ZINC ION × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；PEG 10000, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.10 Å R-free 0.249
1ICI CRYSTAL STRUCTURE OF A SIR2 HOMOLOG-NAD COMPLEX Deposited 2001-04-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–245（245 aa）	Not recorded	ZN ZINC ION × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；PEG 10000, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.10 Å R-free 0.249
1ICI CRYSTAL STRUCTURE OF A SIR2 HOMOLOG-NAD COMPLEX Deposited 2001-04-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–245（245 aa）	Not recorded	ZN ZINC ION × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；PEG 10000, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.10 Å R-free 0.249
1M2G Sir2 homologue-ADP ribose complex Deposited 2002-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–245（245 aa）	Not recorded	ZN ZINC ION × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；291 K；Sodium Citrate, PEG 4000, pH 6.0, EVAPORATION, temperature 291K	Resolution 1.70 Å R-free 0.220
1M2H Sir2 homologue S24A mutant-ADP ribose complex Deposited 2002-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–245（245 aa）	Mutation：S24A	ZN ZINC ION × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.215
1M2J Sir2 homologue H80N mutant-ADP ribose complex Deposited 2002-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–245（245 aa）	Mutation：H80N	ZN ZINC ION × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；291 K；PEG 4000, Sodium Citrate, Isopropanol, pH 6.0, EVAPORATION, temperature 291K	Resolution 1.70 Å R-free 0.218
1M2K Sir2 homologue F159A mutant-ADP ribose complex Deposited 2002-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–245（245 aa）	Mutation：F159A	ZN ZINC ION × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；291 K；PEG 4000, Sodium Citrate, Isopropanol, pH 6.0, EVAPORATION, temperature 291K	Resolution 1.47 Å R-free 0.231
4TWI The structure of Sir2Af1 bound to a succinylated histone peptide Deposited 2014-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–245（245 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris pH 8.5, 200 mM MgCl2, and 20% (w/v) PEG 8,000	Resolution 1.79 Å R-free 0.221

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

View Construct and Data Evidence

UniProt name	NPD1_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–245； UniProt 1–245 Author chain B； PDBConstruct 1–245； UniProt 1–245

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	1m2n
Deposition date deposition_date	2002-06-24
Structure title title	Sir2 homologues (D102G/F159A/R170A) mutant-2'-O-acetyl ADP ribose complex
Keywords keywords	PROTEIN-LIGAND COMPLEX, GENE REGULATION; GENE REGULATION
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	28.00 Å
Radius of gyration Rg (electron density) rg_electron	27.57 Å
Forward intensity I(0) i0	53093000.00
Molecular weight molecular_weight	56125.0 kDa
Excluded volume excluded_volume	70143 Å³
Envelope volume envelope_volume	89205 Å³
Hydration-shell volume shell_volume	27710 Å³
Envelope diameter envelope_diameter	94.8 Å
Shell Rg shell_rg	33.71 Å
Envelope Rg envelope_rg	27.42 Å
Shape Rg shape_rg	27.53 Å
Total Rg total_rg	28.35 Å
Total atoms total_atoms	3930
Residues n_residues	498
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	90.2 Å
Rg (real space) rg_real	28.08 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	5.3090e+07
I(0) uncertainty (real space) i0_real_error	8.1580e+05
Rg (reciprocal space) rg_reciprocal	28.06 Å
I(0) (reciprocal space) i0_reciprocal	53090000.0000
Solution quality estimate total_estimate	0.8864
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.352
Kurtosis Kurtosis kurtosis	-0.554
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18780000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.912

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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	Silent Information Regulator 2
Molecular weight formula_weight	27430.8 kDa
Mutation mutation	D102G, F159A, R170A
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	4088

MDEKLLKTIAESKYLVALTGAGVSAESGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKVWKWYAWRMEKVFNAQPNKAHQAFAELERLGVLKCLITQNVDGLHERAGSRNVIHLHGSLRVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRPGVVWAGEMLPPDVLDAAMREVERADVIIVAGTSAVVQPAASLPLIVKQRGGAIIEINPDETPLTPIADYSLRGKAGEVMDELVRHVRKALSLKLN

来源 Source

来源生物 organism	Archaeoglobus fulgidus
NCBI Class编号 ncbi_taxonomy_id	2234
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	;2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE ;
Molecular weight formula_weight	601.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	158

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1m2na1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.5 — Sir2 family of transcriptional regulators

Domain ID domain_id	d1m2na2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1m2nb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.5 — Sir2 family of transcriptional regulators

Domain ID domain_id	d1m2nb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	1m2nA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	1m2nA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	1m2nB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	1m2nB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

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8. Citations (1)

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Unit-cell length a length_a	84.720 Å
Unit-cell length b length_b	84.720 Å
Unit-cell length c length_c	193.087 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	19.910 Å
R factor r_factor	0.2280
R_work r_work	0.2280
R_free r_free	0.3080

fit	/app/data/saxs_computation/m2/1m2n/1m2n.fit
pddf	/app/data/pr_computation/m2/1m2n/1m2n.pr.out
profile	/app/data/saxs_computation/m2/1m2n/1m2n.dat

Sir2 homologues (D102G/F159A/R170A) mutant-2'-O-acetyl ADP ribose complex

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

Silent Information Regulator 2

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