SAXSdb — 8grf

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

Citrate synthase

Saccharomyces cerevisiae

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–460 Chain B； UniProt 1–460	Not recorded	F-box protein UCC1 × 1 E3 ubiquitin ligase complex SCF subunit × 1 （A0A6A5Q435） EDO 1,2-ETHANEDIOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；70 mM Na citrate pH 5.5, 10.5% (w/v) PEG 6000	Resolution 2.53 Å R-free 0.248

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 8GRF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8GR8 Crystal structure of peroxisomal citrate synthase (Cit2) from Saccharomycescerevisiae Deposited 2022-09-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–460（460 aa） Chain B 1–460（460 aa）	Not recorded	CL CHLORIDE ION × 2 GOL GLYCEROL × 6 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；90 mM KCl, 90 mM HEPES pH 7.5, 13.5% (w/v) PEG 6000	Resolution 2.39 Å R-free 0.228
8GR9 Crystal structure of peroxisomal citrate synthase (Cit2) from Saccharomyces cerevisiae in complex with oxaloacetate and coenzyme-A Deposited 2022-09-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–460（460 aa） Chain B 1–460（460 aa）	Not recorded	COA COENZYME A × 1 GOL GLYCEROL × 3 K POTASSIUM ION × 3 CL CHLORIDE ION × 3 OAA OXALOACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；80 mM KCl, 80 mM HEPES pH 7.5, 12% (w/v) PEG 6000	Resolution 1.48 Å R-free 0.198
8GRE F-box protein in complex with skp1(FL) and substrate Deposited 2022-09-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–460（460 aa） Chain B 1–460（460 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；200 mM Na acetate, 100 mM Na citrate pH 5.5, 10% (w/v) PEG 4000	Resolution 2.30 Å R-free 0.232

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5Q445_YEASX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–460； UniProt 1–460 Author chain B； PDBConstruct 1–460； UniProt 1–460

E3 ubiquitin ligase complex SCF subunit

Saccharomyces cerevisiae

UniProt A0A6A5Q435

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 1–194	Not recorded	Citrate synthase × 2 （A0A6A5Q445） F-box protein UCC1 × 1 EDO 1,2-ETHANEDIOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；70 mM Na citrate pH 5.5, 10.5% (w/v) PEG 6000	Resolution 2.53 Å R-free 0.248

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 8GRF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7PMK S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation I) Deposited 2021-09-02	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain K 1–194（194 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Manual plunger	Resolution 3.20 Å
8GRE F-box protein in complex with skp1(FL) and substrate Deposited 2022-09-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–194（194 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；200 mM Na acetate, 100 mM Na citrate pH 5.5, 10% (w/v) PEG 4000	Resolution 2.30 Å R-free 0.232

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5Q435_YEASX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–194； UniProt 1–194

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	8grf
Deposition date deposition_date	2022-09-01
Structure title title	Crystal structure of F-box protein in the ternary complex with adaptor protein Skp1(DL) and its substrate
Keywords keywords	F-box protein, glyoxylate cycle, E3 ubiquitin ligase, TRANSFERASE, TRANSFERASE-LIGASE complex; TRANSFERASE/LIGASE
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	36.75 Å
Radius of gyration Rg (electron density) rg_electron	36.10 Å
Forward intensity I(0) i0	346930000.00
Molecular weight molecular_weight	155060.0 kDa
Excluded volume excluded_volume	195730 Å³
Envelope volume envelope_volume	250380 Å³
Hydration-shell volume shell_volume	57134 Å³
Envelope diameter envelope_diameter	127.8 Å
Shell Rg shell_rg	43.00 Å
Envelope Rg envelope_rg	36.06 Å
Shape Rg shape_rg	36.08 Å
Total Rg total_rg	36.64 Å
Total atoms total_atoms	10954
Residues n_residues	1362
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	120.3 Å
Rg (real space) rg_real	36.70 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	3.4690e+08
I(0) uncertainty (real space) i0_real_error	5.2160e+06
Rg (reciprocal space) rg_reciprocal	36.73 Å
I(0) (reciprocal space) i0_reciprocal	346900000.0000
Solution quality estimate total_estimate	0.8900
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.0 Å
Skewness Skewness skewness	0.309
Kurtosis Kurtosis kurtosis	-0.411
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	86620000.0000
Real-space data points n_real_points	44
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: 0.996; Smooth: 0.900

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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	Citrate synthase
Molecular weight formula_weight	51476.1 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	11186

MTVPYLNSNRNVASYLQSNSSQEKTLKERFSEIYPIHAQDVRQFVKEHGKTKISDVLLEQVYGGMRGIPGSVWEGSVLDPEDGIRFRGRTIADIQKDLPKAKGSSQPLPEALFWLLLTGEVPTQAQVENLSADLMSRSELPSHVVQLLDNLPKDLHPMAQFSIAVTALESESKFAKAYAQGISKQDYWSYTFEDSLDLLGKLPVIAAKIYRNVFKDGKMGEVDPNADYAKNLVNLIGSKDEDFVDLMRLYLTIHSDHEGGNVSAHTSHLVGSALSSPYLSLASGLNGLAGPLHGRANQEVLEWLFALKEEVNDDYSKDTIEKYLWDTLNSGRVIPGYGHAVLRKTDPRYMAQRKFAMDHFPDYELFKLVSSIYEVAPGVLTEHGKTKNPWPNVDAHSGVLLQYYGLKESSFYTVLFGVSRAFGILAQLITDRAIGASIERPKSYSTEKYKELVKNIESKL

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	F-box protein UCC1
Molecular weight formula_weight	42828.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MNQSDSSLMDLPLEIHLSLLEYVPNELRAVNKYFYVLHNHSYKEKSLAWIAEDNYIWAVVKHSLCLYVKSLDPLRQHAREIIQETKEPGFNVPLCMTKYIADSWYIVYNALQYPGKIINMGWDKYTKSQDLNGSDSTSNFNSRPKERTLMQSLTALPVNFWSRKKDEPTPVNVWFYVKNAHVARYIPKIITEIGICNYGPKQIVASAGYINELITSEGIYCVNLGHLPRLYDEQIFEGTGTTHLPLELKAIDRTDSDVCINSDLVLLGYDFIPYQISKPWLLFRIEPVNSIEAIFNYSECSFSYQFAWSLACLQSEEKISFPRDTIIGHGLPYKPSKLIRIFVYKHPEQKQDLGQEIALPNWNTPYLRR

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	E3 ubiquitin ligase complex SCF subunit
Molecular weight formula_weight	22357.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSKDNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWDREFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEEEAAIRRENEWAEDR

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 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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8. Citations (1)

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Unit-cell length a length_a	77.407 Å
Unit-cell length b length_b	150.976 Å
Unit-cell length c length_c	160.384 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.530 Å
Low-resolution limit resolution_low	36.640 Å
R factor r_factor	0.2164
R_work r_work	0.2153
R_free r_free	0.2477

fit	/app/data/saxs_computation/gr/8grf/8grf.fit
pddf	/app/data/pr_computation/gr/8grf/8grf.pr.out
profile	/app/data/saxs_computation/gr/8grf/8grf.dat

Crystal structure of F-box protein in the ternary complex with adaptor protein Skp1(DL) and its substrate

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

Citrate synthase

State in the Current Structure

Other States of the Same Protein in the Database

E3 ubiquitin ligase complex SCF subunit

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)