SAXSdb — 1bj3

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

PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN B)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 24–146	Fragment：C-TYPE LECTIN CRD DOMAIN	PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN A) × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.8；PROTEIN WAS CRYSTALLIZED BY MIXING WITH EQUAL VOLUME OF 60% AMMONIUM SULPHATE IN 20 MM TRI-HCL BUFFER AT PH 7.8 CONTAINING AND AT ROOM TEMPERATURE	Resolution 2.60 Å R-free 0.271

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 1BJ3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1IXX CRYSTAL STRUCTURE OF COAGULATION FACTORS IX/X-BINDING PROTEIN (IX/X-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS Deposited 1997-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 24–146（123 aa） Fragment：C-TYPE LECTIN DOMAIN Chain D 24–146（123 aa） Fragment：C-TYPE LECTIN DOMAIN Chain F 24–146（123 aa） Fragment：C-TYPE LECTIN DOMAIN	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；60% SATURATED AMMONIUM SULFATE, 20 MM TRIS-HCL, 3 MM CACL2, PH 7.8	Resolution 2.50 Å R-free 0.221
1IXX CRYSTAL STRUCTURE OF COAGULATION FACTORS IX/X-BINDING PROTEIN (IX/X-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS Deposited 1997-05-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 24–146（123 aa） Fragment：C-TYPE LECTIN DOMAIN	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；60% SATURATED AMMONIUM SULFATE, 20 MM TRIS-HCL, 3 MM CACL2, PH 7.8	Resolution 2.50 Å R-free 0.221
1IXX CRYSTAL STRUCTURE OF COAGULATION FACTORS IX/X-BINDING PROTEIN (IX/X-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS Deposited 1997-05-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–146（123 aa） Fragment：C-TYPE LECTIN DOMAIN	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；60% SATURATED AMMONIUM SULFATE, 20 MM TRIS-HCL, 3 MM CACL2, PH 7.8	Resolution 2.50 Å R-free 0.221
1IXX CRYSTAL STRUCTURE OF COAGULATION FACTORS IX/X-BINDING PROTEIN (IX/X-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS Deposited 1997-05-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 24–146（123 aa） Fragment：C-TYPE LECTIN DOMAIN	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；60% SATURATED AMMONIUM SULFATE, 20 MM TRIS-HCL, 3 MM CACL2, PH 7.8	Resolution 2.50 Å R-free 0.221
1J34 Crystal Structure of Mg(II)-and Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein Deposited 2003-01-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 24–146（123 aa）	Not recorded	CA CALCIUM ION × 7 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8；293 K；PEG 6000, Tris-HCl, calcium chloride, magnesium chloride, pH 8, MICROBATCH, temperature 293K	Resolution 1.55 Å R-free 0.212
1J35 Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein Deposited 2003-01-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 24–146（123 aa）	Not recorded	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8；293 K；PEG 6000, Tris-HCl, calcium chloride, pH 8, MICROBATCH, temperature 293K	Resolution 1.80 Å R-free 0.270
1X2T Crystal Structure of Habu IX-bp at pH 6.5 Deposited 2005-04-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–146（123 aa）	Not recorded	CA CALCIUM ION × 2 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 6.5；293 K；PEG 1000, PEG 8000, calcium chloride, MES, pH 6.5, MICROBATCH, temperature 293K	Resolution 1.72 Å R-free 0.222
1X2T Crystal Structure of Habu IX-bp at pH 6.5 Deposited 2005-04-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 24–146（123 aa）	Not recorded	CA CALCIUM ION × 2 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 6.5；293 K；PEG 1000, PEG 8000, calcium chloride, MES, pH 6.5, MICROBATCH, temperature 293K	Resolution 1.72 Å R-free 0.222
1X2W Crystal Structure of Apo-Habu IX-bp at pH 4.6 Deposited 2005-04-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–146（123 aa）	Not recorded	CL CHLORIDE ION × 1 RB RUBIDIUM ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；AMMONIUM SULPHATE, RUBIDIUM ACETATE, PEGMME 2000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.29 Å R-free 0.280
1X2W Crystal Structure of Apo-Habu IX-bp at pH 4.6 Deposited 2005-04-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 24–146（123 aa）	Not recorded	CL CHLORIDE ION × 2 RB RUBIDIUM ION × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；AMMONIUM SULPHATE, RUBIDIUM ACETATE, PEGMME 2000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.29 Å R-free 0.280

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

View Construct and Data Evidence

UniProt name	IXB_TRIFL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–123； UniProt 24–146

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	1bj3
Deposition date deposition_date	1998-07-02
Structure title title	CRYSTAL STRUCTURE OF COAGULATION FACTOR IX-BINDING PROTEIN (IX-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS
Keywords keywords	COAGULATION FACTOR IX-BINDING, HETERODIMER, VENOM, HABU SNAKE, C-TYPE LECTIN SUPERFAMILY, COLLAGEN BINDING PROTEIN; COLLAGEN BINDING PROTEIN
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	22.04 Å
Radius of gyration Rg (electron density) rg_electron	21.41 Å
Forward intensity I(0) i0	15918100.00
Molecular weight molecular_weight	29153.0 kDa
Excluded volume excluded_volume	35842 Å³
Envelope volume envelope_volume	41642 Å³
Hydration-shell volume shell_volume	17431 Å³
Envelope diameter envelope_diameter	83.5 Å
Shell Rg shell_rg	26.52 Å
Envelope Rg envelope_rg	21.65 Å
Shape Rg shape_rg	21.40 Å
Total Rg total_rg	22.11 Å
Total atoms total_atoms	2049
Residues n_residues	252
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	80.4 Å
Rg (real space) rg_real	22.27 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	1.5920e+07
I(0) uncertainty (real space) i0_real_error	2.1830e+05
Rg (reciprocal space) rg_reciprocal	22.22 Å
I(0) (reciprocal space) i0_reciprocal	15920000.0000
Solution quality estimate total_estimate	0.7704
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.4 Å
Skewness Skewness skewness	0.557
Kurtosis Kurtosis kurtosis	-0.266
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6595000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.521; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.509; Smooth: 0.940

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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	PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN A)
Molecular weight formula_weight	14655.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2132

DCPSGWSSYEGHCYKPFKLYKTWDDAERFCTEQAKGGHLVSIESAGEADFVAQLVTENIQNTKSYVWIGLRVQGKEKQCSSEWSDGSSVSYENWIEAESKTCLGLEKETGFRKWVNIYCGQQNPFVCEA

Entity 2 Entity 2 polymer

Description description	PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN B)
Molecular weight formula_weight	14455.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DCPSDWSSYEGHCYKPFSEPKNWADAENFCTQQHAGGHLVSFQSSEEADFVVKLAFQTFGHSIFWMGLSNVWNQCNWQWSNAAMLRYKAWAEESYCVYFKSTNNKWRSRACRMMAQFVCEFQA

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	83

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bj3a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d1bj3b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

CATH v4.4 (2 domains)

Domain ID domain_id	1bj3A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1bj3B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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8. Citations (3)

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Unit-cell length a length_a	58.569 Å
Unit-cell length b length_b	56.794 Å
Unit-cell length c length_c	39.616 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1820
R_work r_work	0.1820
R_free r_free	0.2710

fit	/app/data/saxs_computation/bj/1bj3/1bj3.fit
pddf	/app/data/pr_computation/bj/1bj3/1bj3.pr.out
profile	/app/data/saxs_computation/bj/1bj3/1bj3.dat

CRYSTAL STRUCTURE OF COAGULATION FACTOR IX-BINDING PROTEIN (IX-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS

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

PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN B)

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 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)