SAXSdb — 1ici

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

TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY

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	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–245	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
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–245	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

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 1ICI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1M2G Sir2 homologue-ADP ribose complex Deposited 2002-06-24	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 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 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 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
1M2N Sir2 homologues (D102G/F159A/R170A) mutant-2'-O-acetyl ADP ribose complex Deposited 2002-06-24	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）	Mutation：D102G, F159A, R170A 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
4TWI The structure of Sir2Af1 bound to a succinylated histone peptide Deposited 2014-06-30	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 6 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 12–256； UniProt 1–245 Author chain B； PDBConstruct 12–256； 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	1ici
Deposition date deposition_date	2001-04-01
Structure title title	CRYSTAL STRUCTURE OF A SIR2 HOMOLOG-NAD COMPLEX
Keywords keywords	Rossmann fold, Zinc ribbon, protein deacetylase, NAD-binding, TRANSCRIPTION; TRANSCRIPTION
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	29.30 Å
Radius of gyration Rg (electron density) rg_electron	29.01 Å
Forward intensity I(0) i0	54870900.00
Molecular weight molecular_weight	56866.0 kDa
Excluded volume excluded_volume	70779 Å³
Envelope volume envelope_volume	89438 Å³
Hydration-shell volume shell_volume	27118 Å³
Envelope diameter envelope_diameter	108.0 Å
Shell Rg shell_rg	34.36 Å
Envelope Rg envelope_rg	28.97 Å
Shape Rg shape_rg	29.03 Å
Total Rg total_rg	29.45 Å
Total atoms total_atoms	3988
Residues n_residues	500
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	102.3 Å
Rg (real space) rg_real	29.51 Å
Rg uncertainty (real space) rg_real_error	1.25 Å
I(0) (real space) i0_real	5.4870e+07
I(0) uncertainty (real space) i0_real_error	9.1900e+05
Rg (reciprocal space) rg_reciprocal	29.42 Å
I(0) (reciprocal space) i0_reciprocal	54870000.0000
Solution quality estimate total_estimate	0.7496
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.5 Å
Skewness Skewness skewness	0.494
Kurtosis Kurtosis kurtosis	-0.384
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25450000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.667; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.765; Smooth: 0.000

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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	TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY
Molecular weight formula_weight	28436.7 kDa
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	4249

GSHHHHHHGSHMDEKLLKTIAESKYLVALTGAGVSAESGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKVWKWYAWRMEKVFNAQPNKAHQAFAELERLGVLKCLITQNVDDLHERAGSRNVIHLHGSLRVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRPGVVWFGEMLPPDVLDRAMREVERADVIIVAGTSAVVQPAASLPLIVKQRGGAIIEINPDETPLTPIADYSLRGKAGEVMDELVRHVRKALS

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	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 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	261

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1icia1
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	d1icia2
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	d1icib_
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

CATH v4.4 (4 domains)

Domain ID domain_id	1iciA01
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	1iciA02
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	1iciB01
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	1iciB02
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	65.410 Å
Unit-cell length b length_b	94.540 Å
Unit-cell length c length_c	93.780 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.29 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2030
R_work r_work	0.1990
R_free r_free	0.2490

fit	/app/data/saxs_computation/ic/1ici/1ici.fit
pddf	/app/data/pr_computation/ic/1ici/1ici.pr.out
profile	/app/data/saxs_computation/ic/1ici/1ici.dat

CRYSTAL STRUCTURE OF A SIR2 HOMOLOG-NAD COMPLEX

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

TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY

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