SAXSdb — 1by5

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer 蛋白 2 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：FERRIC HYDROXAMATE UPTAKE PROTEIN × 1 Entity 2：FERRICHROME × 1 缺少 UniProt 身份时不显示参考序列区间	Non-standard monomer：Yes (specific site not provided by mmCIF)	OES N-OCTYL-2-HYDROXYETHYL SULFOXIDE × 8 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.2；pH 6.2	Resolution 2.60 Å R-free 0.229

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	1by5
Deposition date deposition_date	1998-10-23
Structure title title	FHUA FROM E. COLI, WITH ITS LIGAND FERRICHROME
Keywords keywords	FHUA, MEMBRANE PROTEIN, LIGAND-GATED, IRON TRANSPORT, FERRICHROME, METAL BINDING PROTEIN; METAL 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	26.22 Å
Radius of gyration Rg (electron density) rg_electron	25.55 Å
Forward intensity I(0) i0	104271000.00
Molecular weight molecular_weight	79546.0 kDa
Excluded volume excluded_volume	99038 Å³
Envelope volume envelope_volume	118980 Å³
Hydration-shell volume shell_volume	37328 Å³
Envelope diameter envelope_diameter	87.7 Å
Shell Rg shell_rg	34.38 Å
Envelope Rg envelope_rg	25.76 Å
Shape Rg shape_rg	25.56 Å
Total Rg total_rg	26.39 Å
Total atoms total_atoms	5606
Residues n_residues	700
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	84.5 Å
Rg (real space) rg_real	26.09 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.0430e+08
I(0) uncertainty (real space) i0_real_error	1.3890e+06
Rg (reciprocal space) rg_reciprocal	26.13 Å
I(0) (reciprocal space) i0_reciprocal	104300000.0000
Solution quality estimate total_estimate	0.6754
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.2 Å
Skewness Skewness skewness	0.256
Kurtosis Kurtosis kurtosis	-0.245
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23710000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 0.105; Positv: 1.000; Valcen: 0.992; Smooth: 0.967

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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	FERRIC HYDROXAMATE UPTAKE PROTEIN
Molecular weight formula_weight	78929.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5749

AVEPKEDTITVTAAPAPQESAWGPAATIAARQSATGTKTDTPIQKVPQSISVVTAEEMALHQPKSVKEALSYTPGVSVGTRGASNTYDHLIIRGFAAEGQSQNNYLNGLKLQGNFYNDAVIDPYMLERAEIMRGPVSVLYGKSSPGGLLNMVSKRPTTEPLKEVQFKAGTDSLFQTGFDFSDSLDDDGVYSYRLTGLARSANAQQKGSEEQRYAIAPAFTWRPDDKTNFTFLSYFQNEPETGYYGWLPKEGTVEPLPNGKRLPTDFNEGAKNNTYSRNEKMVGYSFDHEFNDTFTVRQNLRFAENKTSQNSVYGYGVCSDPANAYSKQCAALAPADKGHYLARKYVVDDEKLQNFSVDTQLQSKFATGDIDHTLLTGVDFMRMRNDINAWFGYDDSVPLLNLYNPVNTDFDFNAKDPANSGPYRILNKQKQTGVYVQDQAQWDKVLVTLGGRYDWADQESLNRVAGTTDKRDDKQFTWRGGVNYLFDNGVTPYFSYSESFEPSSQVGKDGNIFAPSKGKQYEVGVKYVPEDRPIVVTGAVYNLTKTNNLMADPEGSFFSVEGGEIRARGVEIEAKRPLSASVNVVGSYTYTDAEYTTDTTYKGNTPAQVPKHMASLWADYTFFDGPLSGLTLGTGGRYTGSSYGDPANSFKVGSYTVVDALVRYDLARVGMAGSNVALHVNNLFDREYVASCFNTYGCFWGAERQVVATATFRF

Entity 2 Entity 2 polymer

Description description	FERRICHROME
Molecular weight formula_weight	705.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AAAGGG

Entity 3 Entity 3 non-polymer

Description description	N-OCTYL-2-HYDROXYETHYL SULFOXIDE
Molecular weight formula_weight	206.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 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	143

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1by5a_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.3 — Porins
Family Family family	f.4.3.3 — Ligand-gated protein channel

CATH v4.4 (2 domains)

Domain ID domain_id	1by5A01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	130 — Ferric Hydroxamate Uptake Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — TonB-dependent receptor, plug domain

Domain ID domain_id	1by5A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	170 — Maltoporin; Chain A
Homologous superfamily homologous superfamily	20 — TonB-dependent receptor, beta-barrel domain

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8. Citations (3)

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Unit-cell length a length_a	132.200 Å
Unit-cell length b length_b	89.400 Å
Unit-cell length c length_c	89.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.40 °
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	2.600 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.1840
R_work r_work	0.1840
R_free r_free	0.2290

fit	/app/data/saxs_computation/by/1by5/1by5.fit
pddf	/app/data/pr_computation/by/1by5/1by5.pr.out
profile	/app/data/saxs_computation/by/1by5/1by5.dat

FHUA FROM E. COLI, WITH ITS LIGAND FERRICHROME

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

Assembly Composition of the Current Entry

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)