SAXSdb — 4iup

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

SAWADEE HOMEODOMAIN HOMOLOG 1

Arabidopsis thaliana

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 125–258	Fragment：SHH1 SAWADEE domain (unp residues 125-258) Mutation：L200M, L218M Non-standard monomer：Yes (specific site not provided by mmCIF)	BME BETA-MERCAPTOETHANOL × 1 ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl- -D-Maltoside 7K, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.90 Å R-free 0.194
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 125–258	Fragment：SHH1 SAWADEE domain (unp residues 125-258) Mutation：L200M, L218M Non-standard monomer：Yes (specific site not provided by mmCIF)	BME BETA-MERCAPTOETHANOL × 1 ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl- -D-Maltoside 7K, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.90 Å R-free 0.194

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 4IUP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4IUQ crystal structure of SHH1 SAWADEE domain Deposited 2013-01-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 125–258（134 aa） Fragment：SHH1 SAWADEE domain	Not recorded	ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.81 Å R-free 0.261
4IUQ crystal structure of SHH1 SAWADEE domain Deposited 2013-01-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 125–258（134 aa） Fragment：SHH1 SAWADEE domain	Not recorded	ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.81 Å R-free 0.261
4IUR crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide Deposited 2013-01-21	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 B 125–258（134 aa） Fragment：SHH1 SAWADEE domain (unp residues 125-258)	Not recorded	ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.50 Å R-free 0.256
4IUR crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide Deposited 2013-01-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 125–258（134 aa） Fragment：SHH1 SAWADEE domain (unp residues 125-258)	Not recorded	ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.50 Å R-free 0.256
4IUT crystal structure of SHH1 SAWADEE domain in complex with H3K9me2 peptide Deposited 2013-01-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 125–258（134 aa） Fragment：SHH1 SAWADEE domain (unp residues 125-258)	Not recorded	ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.248
4IUT crystal structure of SHH1 SAWADEE domain in complex with H3K9me2 peptide Deposited 2013-01-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 125–258（134 aa） Fragment：SHH1 SAWADEE domain (unp residues 125-258)	Not recorded	ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.248
4IUU Crystal structure of SHH1 SAWADEE domain in complex with H3K9me1 peptide Deposited 2013-01-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 125–258（134 aa） Fragment：SHH1 SAWADEE domain (unp residues 125-258)	Not recorded	ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.269
4IUU Crystal structure of SHH1 SAWADEE domain in complex with H3K9me1 peptide Deposited 2013-01-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 125–258（134 aa） Fragment：SHH1 SAWADEE domain (unp residues 125-258)	Not recorded	ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.269
4IUV crystal structure of SHH1 SAWADEE domain in complex with H3K4me1K9me1 peptide Deposited 2013-01-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 125–258（134 aa） Fragment：SHH1 SAWADEE domain (unp residues 125-258)	Not recorded	ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.253
4IUV crystal structure of SHH1 SAWADEE domain in complex with H3K4me1K9me1 peptide Deposited 2013-01-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 125–258（134 aa） Fragment：SHH1 SAWADEE domain (unp residues 125-258)	Not recorded	ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.253

5 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9XI47_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–135； UniProt 125–258 Author chain B； PDBConstruct 2–135； UniProt 125–258

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	4iup
Deposition date deposition_date	2013-01-21
Structure title title	crystal structure of Se-substituted arabidopsis thaliana SHH1 SAWADEE domain L200M/L218M mutant
Keywords keywords	tandem tudor, zinc finger, mediate interaction, histone, DNA BINDING PROTEIN, 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	24.37 Å
Radius of gyration Rg (electron density) rg_electron	24.27 Å
Forward intensity I(0) i0	19721700.00
Molecular weight molecular_weight	31722.0 kDa
Excluded volume excluded_volume	38762 Å³
Envelope volume envelope_volume	50450 Å³
Hydration-shell volume shell_volume	19136 Å³
Envelope diameter envelope_diameter	95.9 Å
Shell Rg shell_rg	28.85 Å
Envelope Rg envelope_rg	24.51 Å
Shape Rg shape_rg	24.25 Å
Total Rg total_rg	24.88 Å
Total atoms total_atoms	2202
Residues n_residues	258
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	92.0 Å
Rg (real space) rg_real	24.69 Å
Rg uncertainty (real space) rg_real_error	1.03 Å
I(0) (real space) i0_real	1.9720e+07
I(0) uncertainty (real space) i0_real_error	3.2220e+05
Rg (reciprocal space) rg_reciprocal	24.61 Å
I(0) (reciprocal space) i0_reciprocal	19720000.0000
Solution quality estimate total_estimate	0.7792
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.652
Kurtosis Kurtosis kurtosis	0.123
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2608000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.597; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.451; Smooth: 0.884

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	SAWADEE HOMEODOMAIN HOMOLOG 1
Molecular weight formula_weight	15910.5 kDa
Mutation mutation	L200M, L218M
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	2645

SADLAFEAKSARDYAWYDVSSFLTYRVLRTGELEVRVRFSGFDNRHDEWVNVKTSVRERSIPVEPSECGRVNVGDLMLCFQEREDQALYCDGHVMNIKRGIHDHARCNCVFLVRYELDNTEESLGLERICRRPEE

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	mouse-ear cress,thale-cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	2

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	2

Entity 4 Entity 4 non-polymer

Description description	CYMAL-4
Molecular weight formula_weight	480.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	443

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4iupA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4iupA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	4iupB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4iupB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

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8. Citations (1)

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Unit-cell length a length_a	53.293 Å
Unit-cell length b length_b	56.733 Å
Unit-cell length c length_c	59.299 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.36 °
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	1.900 Å
Low-resolution limit resolution_low	29.599 Å
R factor r_factor	0.1729
R_work r_work	0.1717
R_free r_free	0.1944

fit	/app/data/saxs_computation/iu/4iup/4iup.fit
pddf	/app/data/pr_computation/iu/4iup/4iup.pr.out
profile	/app/data/saxs_computation/iu/4iup/4iup.dat

crystal structure of Se-substituted arabidopsis thaliana SHH1 SAWADEE domain L200M/L218M mutant

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

SAWADEE HOMEODOMAIN HOMOLOG 1

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