SAXSdb — 1txd

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

Rho guanine nucleotide exchange factor 12

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 764–1138	Fragment：DH/PH domains	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG3350, sodium chloride, sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.13 Å R-free 0.274

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 1TXD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1X86 Crystal Structure of the DH/PH domains of Leukemia-associated RhoGEF in complex with RhoA Deposited 2004-08-17	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 764–1138（375 aa） Fragment：DH/PH domains	Mutation：Tyr973Phe	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；PEG8K, sodium phosphate, sodium chloride, EDTA, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.22 Å R-free 0.279
1X86 Crystal Structure of the DH/PH domains of Leukemia-associated RhoGEF in complex with RhoA Deposited 2004-08-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 764–1138（375 aa） Fragment：DH/PH domains	Mutation：Tyr973Phe	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；PEG8K, sodium phosphate, sodium chloride, EDTA, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.22 Å R-free 0.279
1X86 Crystal Structure of the DH/PH domains of Leukemia-associated RhoGEF in complex with RhoA Deposited 2004-08-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 764–1138（375 aa） Fragment：DH/PH domains	Mutation：Tyr973Phe	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；PEG8K, sodium phosphate, sodium chloride, EDTA, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.22 Å R-free 0.279
1X86 Crystal Structure of the DH/PH domains of Leukemia-associated RhoGEF in complex with RhoA Deposited 2004-08-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 764–1138（375 aa） Fragment：DH/PH domains	Mutation：Tyr973Phe	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；PEG8K, sodium phosphate, sodium chloride, EDTA, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.22 Å R-free 0.279
2OMJ solution structure of LARG PDZ domain Deposited 2007-01-22	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 67–151（85 aa） Fragment：PDZ domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；293 K；Ionic strength (raw mmCIF value) 50mM phosphate buffer, 50mM NaCl；Pressure 1 NMR sample composition 1.3mM LARG PDZ domain, 15N, 13C-labeled, 5mM EDTA, 1mM EDTA, 50mM phosphate buffer, 90% H2O, 10% D2O \| 50mM phosphate buffer, 90% H2O, 10% D2O NMR sample composition 1.3mM LARG PDZ domain, 15N, 13C-labeled, 5mM EDTA, 1mM EDTA, 50mM phosphate buffer, 99.9% D2O \| 50mM phosphate buffer, 99.9% D2O	Resolution not provided
2OS6 Solution structure of LARG PDZ domain in complex with C-terminal octa-peptide of Plexin B1 Deposited 2007-02-05	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 67–151（85 aa） Fragment：PDZ domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；293 K；Ionic strength (raw mmCIF value) 50 mM phosphate buffer, 50mM NaCl；Pressure 1 NMR sample composition 0.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide, 50mM phosphate buffer, 90% H2O, 10% D2O \| 50mM phosphate buffer, 90% H2O, 10% D2O NMR sample composition 0.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide, 50mM phosphate buffer, 99.9% D2O \| 50mM phosphate buffer, 99.9% D2O	Resolution not provided

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARHGC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–375； UniProt 764–1138

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	1txd
Deposition date deposition_date	2004-07-03
Structure title title	Crystal Structure of the DH/PH domains of Leukemia-associated RhoGEF
Keywords keywords	helical bundle (DH), beta sandwich (PH), 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	28.01 Å
Radius of gyration Rg (electron density) rg_electron	27.58 Å
Forward intensity I(0) i0	27559300.00
Molecular weight molecular_weight	40996.0 kDa
Excluded volume excluded_volume	51692 Å³
Envelope volume envelope_volume	67750 Å³
Hydration-shell volume shell_volume	21627 Å³
Envelope diameter envelope_diameter	99.5 Å
Shell Rg shell_rg	32.77 Å
Envelope Rg envelope_rg	27.67 Å
Shape Rg shape_rg	27.56 Å
Total Rg total_rg	28.23 Å
Total atoms total_atoms	2881
Residues n_residues	352
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	96.5 Å
Rg (real space) rg_real	28.22 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	2.7560e+07
I(0) uncertainty (real space) i0_real_error	4.2440e+05
Rg (reciprocal space) rg_reciprocal	28.16 Å
I(0) (reciprocal space) i0_reciprocal	27560000.0000
Solution quality estimate total_estimate	0.8395
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.7 Å
Skewness Skewness skewness	0.407
Kurtosis Kurtosis kurtosis	-0.505
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6786000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.766; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.690; Smooth: 0.921

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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1txda1
Class class	a — All alpha proteins
Fold Fold fold	a.87 — DBL homology domain (DH-domain)
Superfamily Superfamily superfamily	a.87.1 — DBL homology domain (DH-domain)
Family Family family	a.87.1.1 — DBL homology domain (DH-domain)

Domain ID domain_id	d1txda2
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.1 — Pleckstrin-homology domain (PH domain)

CATH v4.4 (2 domains)

Domain ID domain_id	1txdA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily	10 — Dbl homology (DH) domain

Domain ID domain_id	1txdA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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Unit-cell length a length_a	193.606 Å
Unit-cell length b length_b	45.859 Å
Unit-cell length c length_c	74.730 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.49 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.130 Å
Low-resolution limit resolution_low	24.850 Å
R factor r_factor	0.2368
R_work r_work	0.2348
R_free r_free	0.2743

Description description	Rho guanine nucleotide exchange factor 12
Molecular weight formula_weight	44694.3 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	2972

Crystal Structure of the DH/PH domains of Leukemia-associated RhoGEF

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

Rho guanine nucleotide exchange factor 12

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	91

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