SAXSdb — 1txu

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

Rab5 GDP/GTP exchange factor

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 133–394	Fragment：VPS9 Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEG 8000, MgCl, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.35 Å R-free 0.269

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 1TXU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2OT3 Crystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21 Deposited 2007-02-07	Different construct Different mutation/modification 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 132–397（266 aa） Fragment：residues 132-297	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；10% PEG 6000, 0.2M MgCl2, 0.05 NaMES Microseeded, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.243
4N3X Crystal structure of Rabex-5 CC domain Deposited 2013-10-08	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 626–672（47 aa） Fragment：Rabex-5 CC domain, UNP residues 626-672	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；289 K；0.10M NaAc, 17.5% MPD, 2% PEG4000 , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.00 Å R-free 0.234
4N3X Crystal structure of Rabex-5 CC domain Deposited 2013-10-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 626–672（47 aa） Fragment：Rabex-5 CC domain, UNP residues 626-672	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；289 K；0.10M NaAc, 17.5% MPD, 2% PEG4000 , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.00 Å R-free 0.234
4N3X Crystal structure of Rabex-5 CC domain Deposited 2013-10-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 626–672（47 aa） Fragment：Rabex-5 CC domain, UNP residues 626-672	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；289 K；0.10M NaAc, 17.5% MPD, 2% PEG4000 , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.00 Å R-free 0.234
4N3X Crystal structure of Rabex-5 CC domain Deposited 2013-10-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 626–672（47 aa） Fragment：Rabex-5 CC domain, UNP residues 626-672	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；289 K；0.10M NaAc, 17.5% MPD, 2% PEG4000 , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.00 Å R-free 0.234
4N3Y Crystal structure of Rabex-5CC and Rabaptin-5C21 complex Deposited 2013-10-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 630–672（43 aa） Fragment：UNP residues 630-672	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.15M MgAc2, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.20 Å R-free 0.234
4N3Z Crystal structure of Rabex-5delta and Rabaptin-5C21 complex Deposited 2013-10-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 132–455（324 aa） Fragment：UNP residues, isoform 2, 132-455	Mutation：residues 387-408 deletion mutant	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；2.0M NaH2PO4/K2HPO4, 0.05% n-octyl-beta-D-galactopyranoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.10 Å R-free 0.315
4Q9U Crystal structure of the Rab5, Rabex-5delta and Rabaptin-5C21 complex Deposited 2014-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 132–455（324 aa） Fragment：UNP residues 132-455 Chain E 132–455（324 aa） Fragment：UNP residues 132-455	Mutation：393-407 deletion mutant Mutation：393-407 deletion mutant	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 5；289 K；1.0M NaH2PO4/K2HPO4, pH 5.0, hanging drop, temperature 289K	Resolution 4.62 Å R-free 0.343

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RABX5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–273； UniProt 133–394

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	1txu
Deposition date deposition_date	2004-07-06
Structure title title	Crystal Structure of the Vps9 Domain of Rabex-5
Keywords keywords	VPS9 DOMAIN, RAB5 GUANINE-NUCLEOTIDE EXCHANGE FACTOR, GEF, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	22.17 Å
Radius of gyration Rg (electron density) rg_electron	21.42 Å
Forward intensity I(0) i0	16428100.00
Molecular weight molecular_weight	30148.0 kDa
Excluded volume excluded_volume	37409 Å³
Envelope volume envelope_volume	45628 Å³
Hydration-shell volume shell_volume	18690 Å³
Envelope diameter envelope_diameter	80.6 Å
Shell Rg shell_rg	27.22 Å
Envelope Rg envelope_rg	21.90 Å
Shape Rg shape_rg	21.44 Å
Total Rg total_rg	22.13 Å
Total atoms total_atoms	2081
Residues n_residues	245
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	77.0 Å
Rg (real space) rg_real	22.31 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.6430e+07
I(0) uncertainty (real space) i0_real_error	2.4290e+05
Rg (reciprocal space) rg_reciprocal	22.28 Å
I(0) (reciprocal space) i0_reciprocal	16430000.0000
Solution quality estimate total_estimate	0.6014
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.0 Å
Skewness Skewness skewness	0.490
Kurtosis Kurtosis kurtosis	-0.207
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3396000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.741; Stabil: 1.000; Sysdev: 0.262; Positv: 1.000; Valcen: 0.806; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Rab5 GDP/GTP exchange factor
Molecular weight formula_weight	32363.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2163

MGHHHHHHGSSIETDRVSKEFIEFLKTFHKTGQEIYKQTKLFLEGMHYKRDLSIEEQSECAQDFYHNVAERMQTRGKVPPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDLAIQKRIRALRWVTPQMLCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHIFNAIKITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCCAVAFIEKLDAQSLNLSQEDFDRYMSGQTSPRKQ

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	82

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1txua_
Class class	a — All alpha proteins
Fold Fold fold	a.222 — VPS9 domain
Superfamily Superfamily superfamily	a.222.1 — VPS9 domain
Family Family family	a.222.1.1 — VPS9 domain

CATH v4.4 (2 domains)

Domain ID domain_id	1txuA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1txuA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	80 — VPS9 domain

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8. Citations (1)

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Unit-cell length a length_a	68.047 Å
Unit-cell length b length_b	88.329 Å
Unit-cell length c length_c	47.299 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2290
R_work r_work	0.2270
R_free r_free	0.2690

fit	/app/data/saxs_computation/tx/1txu/1txu.fit
pddf	/app/data/pr_computation/tx/1txu/1txu.pr.out
profile	/app/data/saxs_computation/tx/1txu/1txu.dat

Crystal Structure of the Vps9 Domain of Rabex-5

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

Rab5 GDP/GTP exchange factor

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