SAXSdb — 1jy2

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

FIBRINOGEN BETA CHAIN

OrganismNot specified

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain O； UniProt 61–116 Chain R； UniProt 61–116	Not recorded	FIBRINOGEN ALPHA CHAIN × 2 FIBRINOGEN GAMMA-B CHAIN × 2 （P12799）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；295 K；PEG 3350, Calcium chloride, Tris, Dioxane, Sodium azide, pH 8.0, VAPOR DIFFUSION, temperature 295K	Resolution 1.40 Å R-free 0.236

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 1JY2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DEQ THE CRYSTAL STRUCTURE OF MODIFIED BOVINE FIBRINOGEN (AT ~4 ANGSTROM RESOLUTION) Deposited 1999-11-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 61–468（408 aa） Fragment：PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT Chain E 61–468（408 aa） Fragment：PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；277 K；10 mM MES, 5mM sodium azide, 2mM calcium chloride , pH 6.2, temperature 277K	Resolution 3.50 Å R-free 0.370
1DEQ THE CRYSTAL STRUCTURE OF MODIFIED BOVINE FIBRINOGEN (AT ~4 ANGSTROM RESOLUTION) Deposited 1999-11-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain O 61–468（408 aa） Fragment：PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT Chain R 61–468（408 aa） Fragment：PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；277 K；10 mM MES, 5mM sodium azide, 2mM calcium chloride , pH 6.2, temperature 277K	Resolution 3.50 Å R-free 0.370
1JY3 Crystal Structure of the Central Region of Bovine Fibrinogen (E5 Fragment) at 1.4 Angstroms Resolution Deposited 2001-09-10	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain O 61–116（56 aa） Chain R 61–116（56 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；295 K；PEG 3350, Calcium chloride, Tris, Dioxane, Sodium azide, pH 8.0, VAPOR DIFFUSION, temperature 295K	Resolution 1.60 Å R-free 0.220
3H32 Crystal structure of D-dimer from human fibrin complexed with Gly-His-Arg-Pro-Tyr-amide Deposited 2009-04-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain M 22–26（5 aa） Fragment：UNP residues 22-26 Chain N 22–26（5 aa） Fragment：UNP residues 22-26	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；Equal volumes of (a) 5 mg/mL D-dimer, 0.5 mM GHRPYam, 0.3 mM GPRPam, 0.05 M Tris-HCl pH 8.0 and (b) 1% PEG 3350, 1 mM Iodoacetamide, 1 mM CaCl2, 2mM Sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.60 Å R-free 0.320

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

View Construct and Data Evidence

UniProt name	FIBB_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain O； PDBConstruct 1–56； UniProt 61–116 Author chain R； PDBConstruct 1–56； UniProt 61–116

FIBRINOGEN GAMMA-B CHAIN

OrganismNot specified

UniProt P12799

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain P； UniProt 25–72 Chain S； UniProt 25–72	Not recorded	FIBRINOGEN ALPHA CHAIN × 2 FIBRINOGEN BETA CHAIN × 2 （P02676）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；295 K；PEG 3350, Calcium chloride, Tris, Dioxane, Sodium azide, pH 8.0, VAPOR DIFFUSION, temperature 295K	Resolution 1.40 Å R-free 0.236

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 1JY2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DEQ THE CRYSTAL STRUCTURE OF MODIFIED BOVINE FIBRINOGEN (AT ~4 ANGSTROM RESOLUTION) Deposited 1999-11-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 25–432（408 aa） Fragment：PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT Chain F 25–432（408 aa） Fragment：PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；277 K；10 mM MES, 5mM sodium azide, 2mM calcium chloride , pH 6.2, temperature 277K	Resolution 3.50 Å R-free 0.370
1DEQ THE CRYSTAL STRUCTURE OF MODIFIED BOVINE FIBRINOGEN (AT ~4 ANGSTROM RESOLUTION) Deposited 1999-11-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain P 25–432（408 aa） Fragment：PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT Chain S 25–432（408 aa） Fragment：PSEUDOMONAS AERUGINOSA PS-1-MODIFIED FRAGMENT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；277 K；10 mM MES, 5mM sodium azide, 2mM calcium chloride , pH 6.2, temperature 277K	Resolution 3.50 Å R-free 0.370
1JY3 Crystal Structure of the Central Region of Bovine Fibrinogen (E5 Fragment) at 1.4 Angstroms Resolution Deposited 2001-09-10	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain P 25–72（48 aa） Chain S 25–72（48 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；295 K；PEG 3350, Calcium chloride, Tris, Dioxane, Sodium azide, pH 8.0, VAPOR DIFFUSION, temperature 295K	Resolution 1.60 Å R-free 0.220

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

View Construct and Data Evidence

UniProt name	FIBG_BOVIN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain P； PDBConstruct 1–48； UniProt 25–72 Author chain S； PDBConstruct 1–48； UniProt 25–72

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	1jy2
Deposition date deposition_date	2001-09-10
Structure title title	Crystal Structure of the Central Region of Bovine Fibrinogen (E5 fragment) at 1.4 Angstroms Resolution
Keywords keywords	fibrinogen, fragment E, disulfide bonds, asymmetry, coiled-coil, beta-sheet, BLOOD CLOTTING; BLOOD CLOTTING
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	23.52 Å
Radius of gyration Rg (electron density) rg_electron	23.79 Å
Forward intensity I(0) i0	19403400.00
Molecular weight molecular_weight	31475.0 kDa
Excluded volume excluded_volume	38575 Å³
Envelope volume envelope_volume	47094 Å³
Hydration-shell volume shell_volume	18885 Å³
Envelope diameter envelope_diameter	96.9 Å
Shell Rg shell_rg	27.56 Å
Envelope Rg envelope_rg	24.37 Å
Shape Rg shape_rg	23.87 Å
Total Rg total_rg	24.02 Å
Total atoms total_atoms	2196
Residues n_residues	278
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	92.1 Å
Rg (real space) rg_real	23.92 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	1.9400e+07
I(0) uncertainty (real space) i0_real_error	2.8210e+05
Rg (reciprocal space) rg_reciprocal	23.83 Å
I(0) (reciprocal space) i0_reciprocal	19400000.0000
Solution quality estimate total_estimate	0.7417
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.7 Å
Skewness Skewness skewness	0.831
Kurtosis Kurtosis kurtosis	0.637
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4975000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.431; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.406; Smooth: 0.938

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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	FIBRINOGEN ALPHA CHAIN
Molecular weight formula_weight	6172.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,Q
Atom count atom_count	2514

SACKETGWPFCSDEDWNTKCPSGCRMKGLIDEVDQDFTSRINKLRDSLFNYQK

Entity 2 Entity 2 polymer

Description description	FIBRINOGEN BETA CHAIN
Molecular weight formula_weight	6253.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,R

KVERKPPDADGCLHADPDLGVLCPTGCKLQDTLVRQERPIRKSIEDLRNTVDSVSR

Entity 3 Entity 3 polymer

Description description	FIBRINOGEN GAMMA-B CHAIN
Molecular weight formula_weight	5476.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,S

YVATRDNCCILDERFGSYCPTTCGIADFLNNYQTSVDKDLRTLEGILY

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	318

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1jy2n_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
Family Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

Domain ID domain_id	d1jy2o_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
Family Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

Domain ID domain_id	d1jy2p_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
Family Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

Domain ID domain_id	d1jy2q_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
Family Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

Domain ID domain_id	d1jy2r_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
Family Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

Domain ID domain_id	d1jy2s_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
Family Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

CATH v4.4 (6 domains)

Domain ID domain_id	1jy2N00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1jy2O00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1jy2P00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1jy2Q00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1jy2R00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1jy2S00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	50 —

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8. Citations (2)

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Unit-cell length a length_a	49.376 Å
Unit-cell length b length_b	66.222 Å
Unit-cell length c length_c	50.658 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.55 °
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	1.400 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	—
R_work r_work	0.2160
R_free r_free	0.2360

fit	/app/data/saxs_computation/jy/1jy2/1jy2.fit
pddf	/app/data/pr_computation/jy/1jy2/1jy2.pr.out
profile	/app/data/saxs_computation/jy/1jy2/1jy2.dat

Crystal Structure of the Central Region of Bovine Fibrinogen (E5 fragment) at 1.4 Angstroms Resolution

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

FIBRINOGEN BETA CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

FIBRINOGEN GAMMA-B CHAIN

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)