SAXSdb — 1b9w

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

PROTEIN (MEROZOITE SURFACE PROTEIN 1)

Plasmodium cynomolgi

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 291–379	Fragment：TWO C-TERMINAL EGF-LIKE DOMAINS	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；pH 5.50	Resolution 1.80 Å R-free 0.279

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q25659_9APIC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–89； UniProt 291–379

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	1b9w
Deposition date deposition_date	1999-02-15
Structure title title	C-TERMINAL MEROZOITE SURFACE PROTEIN 1 FROM PLASMODIUM CYNOMOLGI
Keywords keywords	MSP-1, CANDIDATE MALARIA VACCINE, SURFACE ANTIGEN, SURFACE PROTEIN; SURFACE 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	14.65 Å
Radius of gyration Rg (electron density) rg_electron	13.57 Å
Forward intensity I(0) i0	2575280.00
Molecular weight molecular_weight	10139.0 kDa
Excluded volume excluded_volume	12276 Å³
Envelope volume envelope_volume	15035 Å³
Hydration-shell volume shell_volume	9801 Å³
Envelope diameter envelope_diameter	46.9 Å
Shell Rg shell_rg	18.66 Å
Envelope Rg envelope_rg	13.98 Å
Shape Rg shape_rg	13.58 Å
Total Rg total_rg	14.68 Å
Total atoms total_atoms	701
Residues n_residues	91
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	48.7 Å
Rg (real space) rg_real	14.62 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	2.5750e+06
I(0) uncertainty (real space) i0_real_error	2.9340e+04
Rg (reciprocal space) rg_reciprocal	14.62 Å
I(0) (reciprocal space) i0_reciprocal	2575000.0000
Solution quality estimate total_estimate	0.8963
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.2 Å
Skewness Skewness skewness	0.252
Kurtosis Kurtosis kurtosis	-0.380
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	400200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.998

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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) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1b9wa1
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.4 — Merozoite surface protein 1 (MSP-1)

Domain ID domain_id	d1b9wa2
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.4 — Merozoite surface protein 1 (MSP-1)

Domain ID domain_id	d1b9wa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	1b9wA01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	1b9wA02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

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8. Citations (1)

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Unit-cell length a length_a	43.770 Å
Unit-cell length b length_b	43.770 Å
Unit-cell length c length_c	92.040 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2120
R_free r_free	0.2790

Description description	PROTEIN (MEROZOITE SURFACE PROTEIN 1)
Molecular weight formula_weight	10795.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	766

C-TERMINAL MEROZOITE SURFACE PROTEIN 1 FROM PLASMODIUM CYNOMOLGI

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

PROTEIN (MEROZOITE SURFACE PROTEIN 1)

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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Plasmodium cynomolgi
NCBI Class编号 ncbi_taxonomy_id	5827
宿主生物 host_organism	Trichoplusia ni

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

fit	/app/data/saxs_computation/b9/1b9w/1b9w.fit
pddf	/app/data/pr_computation/b9/1b9w/1b9w.pr.out
profile	/app/data/saxs_computation/b9/1b9w/1b9w.dat