SAXSdb — 5c5s

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

Unconventional myosin-IXb

Homo sapiens

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 1691–1916	Fragment：UNP residues 1691-1916	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.2 M NH4Ac, 0.1 M Bis-Tris and 20% w/v PEG 3350	Resolution 2.20 Å R-free 0.246
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1691–1916	Fragment：UNP residues 1691-1916	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.2 M NH4Ac, 0.1 M Bis-Tris and 20% w/v PEG 3350	Resolution 2.20 Å R-free 0.246
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1691–1916	Fragment：UNP residues 1691-1916	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.2 M NH4Ac, 0.1 M Bis-Tris and 20% w/v PEG 3350	Resolution 2.20 Å R-free 0.246
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1691–1916	Fragment：UNP residues 1691-1916	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.2 M NH4Ac, 0.1 M Bis-Tris and 20% w/v PEG 3350	Resolution 2.20 Å R-free 0.246

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 5C5S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5HPY Crystal Structure of RhoA.GDP.MgF3-in complex with human Myosin 9b RhoGAP domain Deposited 2016-01-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1691–1916（226 aa）	Not recorded	MGF TRIFLUOROMAGNESATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；20% (w/v) PEG 3350, 0.2M sodium malonate pH 7.0.	Resolution 2.40 Å R-free 0.246
5HPY Crystal Structure of RhoA.GDP.MgF3-in complex with human Myosin 9b RhoGAP domain Deposited 2016-01-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1691–1916（226 aa）	Not recorded	MGF TRIFLUOROMAGNESATE × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；20% (w/v) PEG 3350, 0.2M sodium malonate pH 7.0.	Resolution 2.40 Å R-free 0.246

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

View Construct and Data Evidence

UniProt name	MYO9B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–232； UniProt 1691–1916 Author chain B； PDBConstruct 7–232； UniProt 1691–1916 Author chain C； PDBConstruct 7–232； UniProt 1691–1916 Author chain D； PDBConstruct 7–232； UniProt 1691–1916

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	5c5s
Deposition date deposition_date	2015-06-22
Structure title title	Crystal Structure of human Myosin 9b RhoGAP domain at 2.2 angstrom
Keywords keywords	RhoGAP domain, SIGNALING PROTEIN; SIGNALING 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	31.79 Å
Radius of gyration Rg (electron density) rg_electron	30.81 Å
Forward intensity I(0) i0	124605000.00
Molecular weight molecular_weight	91447.0 kDa
Excluded volume excluded_volume	115800 Å³
Envelope volume envelope_volume	146900 Å³
Hydration-shell volume shell_volume	39738 Å³
Envelope diameter envelope_diameter	114.8 Å
Shell Rg shell_rg	37.91 Å
Envelope Rg envelope_rg	30.56 Å
Shape Rg shape_rg	30.81 Å
Total Rg total_rg	31.43 Å
Total atoms total_atoms	6417
Residues n_residues	817
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	107.8 Å
Rg (real space) rg_real	31.71 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	1.2460e+08
I(0) uncertainty (real space) i0_real_error	1.7490e+06
Rg (reciprocal space) rg_reciprocal	31.75 Å
I(0) (reciprocal space) i0_reciprocal	124600000.0000
Solution quality estimate total_estimate	0.8837
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.8 Å
Skewness Skewness skewness	0.273
Kurtosis Kurtosis kurtosis	-0.329
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27360000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.991

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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) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d5c5sa1
Class class	a — All alpha proteins
Fold Fold fold	a.116 — GTPase activation domain, GAP
Superfamily Superfamily superfamily	a.116.1 — GTPase activation domain, GAP
Family Family family	a.116.1.0 — automated matches

Domain ID domain_id	d5c5sa2
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

Domain ID domain_id	d5c5sb_
Class class	a — All alpha proteins
Fold Fold fold	a.116 — GTPase activation domain, GAP
Superfamily Superfamily superfamily	a.116.1 — GTPase activation domain, GAP
Family Family family	a.116.1.0 — automated matches

Domain ID domain_id	d5c5sc_
Class class	a — All alpha proteins
Fold Fold fold	a.116 — GTPase activation domain, GAP
Superfamily Superfamily superfamily	a.116.1 — GTPase activation domain, GAP
Family Family family	a.116.1.0 — automated matches

Domain ID domain_id	d5c5sd_
Class class	a — All alpha proteins
Fold Fold fold	a.116 — GTPase activation domain, GAP
Superfamily Superfamily superfamily	a.116.1 — GTPase activation domain, GAP
Family Family family	a.116.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	5c5sA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily	10 — Rho GTPase activation protein

Domain ID domain_id	5c5sB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily	10 — Rho GTPase activation protein

Domain ID domain_id	5c5sC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily	10 — Rho GTPase activation protein

Domain ID domain_id	5c5sD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily	10 — Rho GTPase activation protein

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8. Citations (1)

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Unit-cell length a length_a	77.084 Å
Unit-cell length b length_b	84.984 Å
Unit-cell length c length_c	134.139 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	39.570 Å
R factor r_factor	0.2225
R_work r_work	0.2214
R_free r_free	0.2459

Description description	Unconventional myosin-IXb
Molecular weight formula_weight	26060.3 kDa
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	6824

Crystal Structure of human Myosin 9b RhoGAP domain at 2.2 angstrom

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

Unconventional myosin-IXb

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) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	353

fit	/app/data/saxs_computation/c5/5c5s/5c5s.fit
pddf	/app/data/pr_computation/c5/5c5s/5c5s.pr.out
profile	/app/data/saxs_computation/c5/5c5s/5c5s.dat