SAXSdb — 5jgc

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

Protein TPR1

Oryza sativa

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–209	Fragment：N-terminal topless domain (UNP residues 1-209)	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；15% w/v Polyethylene glycol 4000, 0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride pH 8.5	Resolution 2.08 Å R-free 0.246

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 5JGC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4ZHE Crystal structure of the SeMet substituted Topless related protein 2 (TPR2) N-terminal domain (1-209) from rice Deposited 2015-04-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–209（209 aa） Fragment：N-TERMINAL DOMAIN (UNP residues 1-209) Chain B 1–209（209 aa） Fragment：N-TERMINAL DOMAIN (UNP residues 1-209) Chain C 1–209（209 aa） Fragment：N-TERMINAL DOMAIN (UNP residues 1-209) Chain D 1–209（209 aa） Fragment：N-TERMINAL DOMAIN (UNP residues 1-209)	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% w/v PEG 3,350, 0.2 M Magnesium chloride, 0.1 M BIS-TRIS, pH 6.5, 19.6 mM 5-Methyl-6-O-(N-heptylcarbamoyl)-alpha-D-glucopyranoside	Resolution 2.50 Å R-free 0.242
5C6Q Crystal structure of the apo TOPLESS related protein 2 (TPR2) N-terminal domain (1-209) from rice Deposited 2015-06-23	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG 3350, 0.2 M magnesium chloride, 0.1 M BIS-TRIS, pH 6.5	Resolution 3.25 Å R-free 0.270
5C6V Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209) in complex with Arabidopsis NINJA peptide Deposited 2015-06-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain B 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain C 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain D 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% w/v PEG 3,350, 0.2 M NaCl, 0.1 M BIS-TRIS pH 5.5, 3.0% w/v D-(+)-glucose monohydrate	Resolution 3.10 Å R-free 0.286
5C7E Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209) in complex with Arabidopsis IAA10 peptide Deposited 2015-06-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain B 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain C 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain D 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% w/v PEG 3,350, 0.2 M sodium citrate tribasic dihydrate	Resolution 3.10 Å R-free 0.229
5C7E Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209) in complex with Arabidopsis IAA10 peptide Deposited 2015-06-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain F 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% w/v PEG 3,350, 0.2 M sodium citrate tribasic dihydrate	Resolution 3.10 Å R-free 0.229
5C7F Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209) in complex with Arabidopsis IAA1 peptide Deposited 2015-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain B 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain C 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209) Chain D 1–209（209 aa） Fragment：N-terminal domain (UNP residues 1-209)	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% w/v PEG 3,350, 0.2 M NaCl, 0.1 M BIS-TRIS pH 5.5	Resolution 2.70 Å R-free 0.256
5J9K Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) in complex with rice D53 repressor EAR peptide motif Deposited 2016-04-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209) Chain B 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% w/v Polyethylene glycol 3350, 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS, pH 6.5	Resolution 2.55 Å R-free 0.253
5JA5 Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) L111A and L130A mutant in complex with rice D53 repressor EAR peptide motif Deposited 2016-04-12	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；293 K；20% w/v Polyethylene glycol 3350, 0.2 M Potassium phosphate monobasic, pH 4.8	Resolution 2.00 Å R-free 0.228
5JHP Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) L179A and I195A mutant in complex with rice D53 repressor EAR peptide motif Deposited 2016-04-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209) Chain B 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209) Chain C 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209) Chain D 1–209（209 aa） Fragment：N-terminal topless domain (UNP residues 1-209)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；20% w/v Polyethylene glycol 3350, 0.2 M Lithium sulfate monohydrate, pH 6.0	Resolution 3.15 Å R-free 0.284

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TPR1_ORYSJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–209； UniProt 1–209

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	5jgc
Deposition date deposition_date	2016-04-20
Structure title title	Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) L111A, L130A, L179A and I195A mutant
Keywords keywords	;TRANSCRIPTION REPRESSION, TRANSCRIPTIONAL COREPRESSOR TOPLESS, ALPHA-HELICAL STRUCTURE, TETRAMER, TRANSCRIPTIONAL REPRESSOR D53, 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	23.91 Å
Radius of gyration Rg (electron density) rg_electron	23.28 Å
Forward intensity I(0) i0	9387270.00
Molecular weight molecular_weight	23306.0 kDa
Excluded volume excluded_volume	29400 Å³
Envelope volume envelope_volume	37857 Å³
Hydration-shell volume shell_volume	15833 Å³
Envelope diameter envelope_diameter	93.7 Å
Shell Rg shell_rg	26.35 Å
Envelope Rg envelope_rg	24.17 Å
Shape Rg shape_rg	23.18 Å
Total Rg total_rg	24.04 Å
Total atoms total_atoms	1641
Residues n_residues	199
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	90.4 Å
Rg (real space) rg_real	24.50 Å
Rg uncertainty (real space) rg_real_error	1.20 Å
I(0) (real space) i0_real	9.3870e+06
I(0) uncertainty (real space) i0_real_error	1.4650e+05
Rg (reciprocal space) rg_reciprocal	24.36 Å
I(0) (reciprocal space) i0_reciprocal	9386000.0000
Solution quality estimate total_estimate	0.7094
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.815
Kurtosis Kurtosis kurtosis	0.163
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1202000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.365; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.189; Smooth: 0.933

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protein TPR1
Molecular weight formula_weight	24735.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1711

MSSLSRELVFLILQFLDEEKFKETVHKLEQESGFFFNMKYFEEKVHAGEWDEVEKYLSGFTKVDDNRYSMKIFFEIRKQKYLEALDRHDRAKAVDILVKDLKVFSTFNEEAYKEITQLLTLENFRENEQASKYGDTKSARSIMLIELKKLIEANPLFREKLVFPTLKASRLRTLINQSANWQHQLCKNPRPNPDAKTLFTDHTCTPPNG

来源 Source

来源生物 organism	Oryza sativa
通用名 common_name	Rice
NCBI Class编号 ncbi_taxonomy_id	4530
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	nat
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	70

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8. Citations (2)

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Unit-cell length a length_a	57.516 Å
Unit-cell length b length_b	57.516 Å
Unit-cell length c length_c	174.937 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	8

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	27.319 Å
R factor r_factor	0.2115
R_work r_work	0.2098
R_free r_free	0.2457

fit	/app/data/saxs_computation/jg/5jgc/5jgc.fit
pddf	/app/data/pr_computation/jg/5jgc/5jgc.pr.out
profile	/app/data/saxs_computation/jg/5jgc/5jgc.dat

Crystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) L111A, L130A, L179A and I195A mutant

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

Protein TPR1

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