SAXSdb — 1u2m

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

Histone-like protein HLP-1

Escherichia coli

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 21–161 Chain B； UniProt 21–161 Chain C； UniProt 21–161	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 350 monomethy ether, ammonium dihydrogen phosphate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.259

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 1U2M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1SG2 Crystal structure of the periplasmic chaperone Skp Deposited 2004-02-23	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 21–161（141 aa） Chain B 21–161（141 aa） Chain C 21–161（141 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；34.5% (v/v) ethanol, 7% (w/v) polyethylene glycol 1000, 50 mM Na-phosphate, 50 mM Na-citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.279

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

View Construct and Data Evidence

UniProt name	HLPA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–143； UniProt 21–161 Author chain B； PDBConstruct 3–143； UniProt 21–161 Author chain C； PDBConstruct 3–143； UniProt 21–161

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	1u2m
Deposition date deposition_date	2004-07-19
Structure title title	Crystal Structure of Skp
Keywords keywords	coiled coil, chaperone; CHAPERONE
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	27.92 Å
Radius of gyration Rg (electron density) rg_electron	27.14 Å
Forward intensity I(0) i0	27418900.00
Molecular weight molecular_weight	37845.0 kDa
Excluded volume excluded_volume	46379 Å³
Envelope volume envelope_volume	70298 Å³
Hydration-shell volume shell_volume	22694 Å³
Envelope diameter envelope_diameter	93.8 Å
Shell Rg shell_rg	32.67 Å
Envelope Rg envelope_rg	26.38 Å
Shape Rg shape_rg	27.04 Å
Total Rg total_rg	28.07 Å
Total atoms total_atoms	2615
Residues n_residues	335
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	90.5 Å
Rg (real space) rg_real	27.96 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	2.7420e+07
I(0) uncertainty (real space) i0_real_error	4.2330e+05
Rg (reciprocal space) rg_reciprocal	27.95 Å
I(0) (reciprocal space) i0_reciprocal	27420000.0000
Solution quality estimate total_estimate	0.8815
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.5 Å
Skewness Skewness skewness	0.316
Kurtosis Kurtosis kurtosis	-0.279
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1709000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.847

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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) 8 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1u2ma1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.48 — OmpH-like
Superfamily Superfamily superfamily	f.48.1 — OmpH-like
Family Family family	f.48.1.1 — OmpH-like

Domain ID domain_id	d1u2ma2
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	d1u2mb_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.48 — OmpH-like
Superfamily Superfamily superfamily	f.48.1 — OmpH-like
Family Family family	f.48.1.1 — OmpH-like

Domain ID domain_id	d1u2mc1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.48 — OmpH-like
Superfamily Superfamily superfamily	f.48.1 — OmpH-like
Family Family family	f.48.1.1 — OmpH-like

Domain ID domain_id	d1u2mc2
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 (3 domains)

Domain ID domain_id	1u2mA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	910 — Protein Binding, DinI Protein; Chain A
Homologous superfamily homologous superfamily	20 — Skp domain

Domain ID domain_id	1u2mB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	910 — Protein Binding, DinI Protein; Chain A
Homologous superfamily homologous superfamily	20 — Skp domain

Domain ID domain_id	1u2mC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	910 — Protein Binding, DinI Protein; Chain A
Homologous superfamily homologous superfamily	20 — Skp domain

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8. Citations (1)

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Unit-cell length a length_a	55.828 Å
Unit-cell length b length_b	84.190 Å
Unit-cell length c length_c	160.181 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	12

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	58.030 Å
R factor r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.2590

Description description	Histone-like protein HLP-1
Molecular weight formula_weight	16185.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2662

Crystal Structure of Skp

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

Histone-like protein HLP-1

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) 8 domains

SCOP 2.08 (5 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
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	47

fit	/app/data/saxs_computation/u2/1u2m/1u2m.fit
pddf	/app/data/pr_computation/u2/1u2m/1u2m.pr.out
profile	/app/data/saxs_computation/u2/1u2m/1u2m.dat