SAXSdb — 2gcj

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

Hypothetical 63.0 kDa protein in DAK1-ORC1 intergenic region

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 220–478	Fragment：Pob3 Middle domain Mutation：Q308K	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；21% PEG 3350, 20% Glycerol, 200mM NaCl, 50mM Ammonium Sulphate, 100mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.55 Å R-free 0.303
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 220–478	Fragment：Pob3 Middle domain Mutation：Q308K	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；21% PEG 3350, 20% Glycerol, 200mM NaCl, 50mM Ammonium Sulphate, 100mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.55 Å R-free 0.303
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 220–478	Fragment：Pob3 Middle domain Mutation：Q308K	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；21% PEG 3350, 20% Glycerol, 200mM NaCl, 50mM Ammonium Sulphate, 100mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.55 Å R-free 0.303
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 220–478	Fragment：Pob3 Middle domain Mutation：Q308K	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；21% PEG 3350, 20% Glycerol, 200mM NaCl, 50mM Ammonium Sulphate, 100mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.55 Å R-free 0.303

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 2GCJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2GCL Structure of the Pob3 Middle domain Deposited 2006-03-14	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 A 220–478（259 aa） Fragment：Middle domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；21% PEG 3350, 20% glycerol, 200mM NaCl, 50mM Ammonium sulphate, 100mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.21 Å R-free 0.264
2GCL Structure of the Pob3 Middle domain Deposited 2006-03-14	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 220–478（259 aa） Fragment：Middle domain	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 7.5；298 K；21% PEG 3350, 20% glycerol, 200mM NaCl, 50mM Ammonium sulphate, 100mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.21 Å R-free 0.264
3F5R The crystal structure of a subunit of the heterodimeric FACT complex (Spt16p-Pob3p). Deposited 2008-11-04	Different construct Different mutation/modification 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 1–168（168 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 2 FMT FORMIC ACID × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Bis-tris, 1.5M (NH4)2SO4., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.70 Å R-free 0.192
4PQ0 Crystal structure of POB3 middle domain at 1.65A Deposited 2014-02-28	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 A 232–473（242 aa） Fragment：UNP RESIDUES 232-473	Not recorded	MLA MALONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；287 K；0.1M Sodium malonate pH 7.0, 0.1M Ammonium acetate, 20% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 1.65 Å R-free 0.248
8XGC Structure of yeast replisome associated with FACT and histone hexamer, Composite map Deposited 2023-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric	Chain M 1–552（552 aa）	Not recorded	ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

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

View Construct and Data Evidence

UniProt name	YMG9_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–261； UniProt 220–478 Author chain B； PDBConstruct 3–261； UniProt 220–478 Author chain C； PDBConstruct 3–261； UniProt 220–478 Author chain D； PDBConstruct 3–261； UniProt 220–478

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	2gcj
Deposition date deposition_date	2006-03-14
Structure title title	Crystal Structure of the Pob3 middle domain
Keywords keywords	Chromatin, FACT, double PH domain, REPLICATION; REPLICATION
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	35.13 Å
Radius of gyration Rg (electron density) rg_electron	34.28 Å
Forward intensity I(0) i0	168786000.00
Molecular weight molecular_weight	107040.0 kDa
Excluded volume excluded_volume	135370 Å³
Envelope volume envelope_volume	183600 Å³
Hydration-shell volume shell_volume	45366 Å³
Envelope diameter envelope_diameter	125.3 Å
Shell Rg shell_rg	40.14 Å
Envelope Rg envelope_rg	33.87 Å
Shape Rg shape_rg	34.24 Å
Total Rg total_rg	34.90 Å
Total atoms total_atoms	7569
Residues n_residues	919
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	116.0 Å
Rg (real space) rg_real	35.05 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	1.6880e+08
I(0) uncertainty (real space) i0_real_error	2.4870e+06
Rg (reciprocal space) rg_reciprocal	35.10 Å
I(0) (reciprocal space) i0_reciprocal	168800000.0000
Solution quality estimate total_estimate	0.8897
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.8 Å
Skewness Skewness skewness	0.258
Kurtosis Kurtosis kurtosis	-0.340
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	35860000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.935

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2gcja1
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.10 — SSRP1-like

Domain ID domain_id	d2gcjb_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.10 — SSRP1-like

Domain ID domain_id	d2gcjc_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.10 — SSRP1-like

Domain ID domain_id	d2gcjd_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.10 — SSRP1-like

CATH v4.4 (8 domains)

Domain ID domain_id	2gcjA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	2gcjA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	2gcjB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	2gcjB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	2gcjC01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	2gcjC02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	2gcjD01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	2gcjD02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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Unit-cell length a length_a	57.868 Å
Unit-cell length b length_b	157.527 Å
Unit-cell length c length_c	57.787 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	89.77 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	78.810 Å
R factor r_factor	0.2193
R_work r_work	0.2147
R_free r_free	0.3029

Description description	Hypothetical 63.0 kDa protein in DAK1-ORC1 intergenic region
Molecular weight formula_weight	30341.3 kDa
Mutation mutation	Q308K
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7649

Crystal Structure of the Pob3 middle domain

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

Hypothetical 63.0 kDa protein in DAK1-ORC1 intergenic region

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	80

fit	/app/data/saxs_computation/gc/2gcj/2gcj.fit
pddf	/app/data/pr_computation/gc/2gcj/2gcj.pr.out
profile	/app/data/saxs_computation/gc/2gcj/2gcj.dat