SAXSdb — 6bnm

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

Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 2 protein

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 219–377	Not recorded	CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.1 M Sodium Acetate pH 5, 3.325 M Sodium Chloride	Resolution 1.90 Å R-free 0.232

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	PREX2_HUMAN
Isoform	Q70Z35-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–162； UniProt 219–377

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	6bnm
Deposition date deposition_date	2017-11-17
Structure title title	Crystal Structure of the P-Rex2 PH domain
Keywords keywords	pleckstrin homology domain, beta sandwich, phosphatidylinositol-binding, LIPID BINDING PROTEIN; LIPID 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	16.30 Å
Radius of gyration Rg (electron density) rg_electron	15.02 Å
Forward intensity I(0) i0	5372770.00
Molecular weight molecular_weight	16272.0 kDa
Excluded volume excluded_volume	20169 Å³
Envelope volume envelope_volume	23210 Å³
Hydration-shell volume shell_volume	13261 Å³
Envelope diameter envelope_diameter	53.4 Å
Shell Rg shell_rg	20.55 Å
Envelope Rg envelope_rg	15.32 Å
Shape Rg shape_rg	15.03 Å
Total Rg total_rg	16.03 Å
Total atoms total_atoms	1139
Residues n_residues	137
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	55.4 Å
Rg (real space) rg_real	16.21 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	5.3730e+06
I(0) uncertainty (real space) i0_real_error	6.6860e+04
Rg (reciprocal space) rg_reciprocal	16.22 Å
I(0) (reciprocal space) i0_reciprocal	5373000.0000
Solution quality estimate total_estimate	0.8692
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.3 Å
Skewness Skewness skewness	0.192
Kurtosis Kurtosis kurtosis	-0.264
Angular range angular_range	— – 0.4900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	942900.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.994

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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	Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 2 protein
Molecular weight formula_weight	19066.8 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	1213

GEFEKLEVLEEWQSHIEGWEGSNITDTCTEMLMCGVLLKISSGNIQERVFFLFDNLLVYCKRKHRRLKNSKASTDGHRYLFRGRINTEVMEVENVDDGTADFHSSGHIVVNGWKIHNTAKNKWFVCMAKTPEEKHEWFEAILKERERRKGLKLGMEQDTWVM

来源 Source

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-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	74

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6bnma1
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.55.1.0 — automated matches

Domain ID domain_id	d6bnma2
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 (1 domains)

Domain ID domain_id	6bnmA00
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	60.105 Å
Unit-cell length b length_b	60.105 Å
Unit-cell length c length_c	86.238 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	52.050 Å
R factor r_factor	0.1928
R_work r_work	0.1908
R_free r_free	0.2316

fit	/app/data/saxs_computation/bn/6bnm/6bnm.fit
pddf	/app/data/pr_computation/bn/6bnm/6bnm.pr.out
profile	/app/data/saxs_computation/bn/6bnm/6bnm.dat

Crystal Structure of the P-Rex2 PH domain

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

Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 2 protein

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