SAXSdb — 1d1j

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

PROFILIN II

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–140 Chain B； UniProt 2–140 Chain C； UniProt 2–140 Chain D； UniProt 2–140	Not recorded	SO4 SULFATE ION × 4 PG6 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE × 1 PG5 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；277 K；MAGNESIUM SULFATE, PEG400, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.268

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	PROF2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–139； UniProt 2–140 Author chain B； PDBConstruct 1–139； UniProt 2–140 Author chain C； PDBConstruct 1–139； UniProt 2–140 Author chain D； PDBConstruct 1–139； UniProt 2–140

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	1d1j
Deposition date deposition_date	1999-09-17
Structure title title	CRYSTAL STRUCTURE OF HUMAN PROFILIN II
Keywords keywords	ACIDIC PROFILIN ISOFORM, ACTIN-BINDING PROTEIN, POLY-L-PROLINE BINDING PROTEIN, CONTRACTILE PROTEIN; CONTRACTILE 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	25.66 Å
Radius of gyration Rg (electron density) rg_electron	24.75 Å
Forward intensity I(0) i0	61052800.00
Molecular weight molecular_weight	59125.0 kDa
Excluded volume excluded_volume	73308 Å³
Envelope volume envelope_volume	87854 Å³
Hydration-shell volume shell_volume	29293 Å³
Envelope diameter envelope_diameter	84.4 Å
Shell Rg shell_rg	32.19 Å
Envelope Rg envelope_rg	24.80 Å
Shape Rg shape_rg	24.74 Å
Total Rg total_rg	25.56 Å
Total atoms total_atoms	4125
Residues n_residues	549
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	82.8 Å
Rg (real space) rg_real	25.56 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	6.1050e+07
I(0) uncertainty (real space) i0_real_error	8.3760e+05
Rg (reciprocal space) rg_reciprocal	25.60 Å
I(0) (reciprocal space) i0_reciprocal	61050000.0000
Solution quality estimate total_estimate	0.8947
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.0 Å
Skewness Skewness skewness	0.199
Kurtosis Kurtosis kurtosis	-0.488
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	39270000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.961

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	PROFILIN II
Molecular weight formula_weight	14973.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4516

AGWQSYVDNLMCDGCCQEAAIVGYCDAKYVWAATAGGVFQSITPIEIDMIVGKDREGFFTNGLTLGAKKCSVIRDSLYVDGDCTMDIRTKSQGGEPTYNVAVGRAGRALVIVMGKEGVHGGTLNKKAYELALYLRRSDV

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

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
Molecular weight formula_weight	266.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
Molecular weight formula_weight	178.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	391

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1d1ja_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.1 — Profilin (actin-binding protein)
Family Family family	d.110.1.1 — Profilin (actin-binding protein)

Domain ID domain_id	d1d1jb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.1 — Profilin (actin-binding protein)
Family Family family	d.110.1.1 — Profilin (actin-binding protein)

Domain ID domain_id	d1d1jc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.1 — Profilin (actin-binding protein)
Family Family family	d.110.1.1 — Profilin (actin-binding protein)

Domain ID domain_id	d1d1jd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.1 — Profilin (actin-binding protein)
Family Family family	d.110.1.1 — Profilin (actin-binding protein)

CATH v4.4 (4 domains)

Domain ID domain_id	1d1jA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	1d1jB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	1d1jC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

Domain ID domain_id	1d1jD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

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8. Citations (1)

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Unit-cell length a length_a	71.140 Å
Unit-cell length b length_b	44.800 Å
Unit-cell length c length_c	89.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2200
R_work r_work	0.2160
R_free r_free	0.2680

fit	/app/data/saxs_computation/d1/1d1j/1d1j.fit
pddf	/app/data/pr_computation/d1/1d1j/1d1j.pr.out
profile	/app/data/saxs_computation/d1/1d1j/1d1j.dat

CRYSTAL STRUCTURE OF HUMAN PROFILIN II

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

PROFILIN II

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