SAXSdb — 1b4h

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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：PERIPLASMIC OLIGO-PEPTIDE BINDING PROTEIN × 1 Entity 2：LYS-DAB-LYS PEPTIDE × 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)	U1 URANIUM ATOM × 8	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；pH 5.5	Resolution 1.90 Å R-free 0.230

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	1b4h
Deposition date deposition_date	1998-11-11
Structure title title	OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-DIAMINOBUTYRIC ACID-LYSINE
Keywords keywords	PERIPLASMIC PEPTIDE BINDING PROTEIN, PEPTIDE BINDING PROTEIN; PEPTIDE 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	24.43 Å
Radius of gyration Rg (electron density) rg_electron	23.17 Å
Forward intensity I(0) i0	64331800.00
Molecular weight molecular_weight	61082.0 kDa
Excluded volume excluded_volume	74953 Å³
Envelope volume envelope_volume	84638 Å³
Hydration-shell volume shell_volume	29750 Å³
Envelope diameter envelope_diameter	80.1 Å
Shell Rg shell_rg	30.98 Å
Envelope Rg envelope_rg	23.32 Å
Shape Rg shape_rg	22.97 Å
Total Rg total_rg	24.55 Å
Total atoms total_atoms	4199
Residues n_residues	519
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	75.8 Å
Rg (real space) rg_real	24.30 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	6.4330e+07
I(0) uncertainty (real space) i0_real_error	8.6650e+05
Rg (reciprocal space) rg_reciprocal	24.33 Å
I(0) (reciprocal space) i0_reciprocal	64330000.0000
Solution quality estimate total_estimate	0.9028
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.224
Kurtosis Kurtosis kurtosis	-0.395
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10240000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.974

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PERIPLASMIC OLIGO-PEPTIDE BINDING PROTEIN
Molecular weight formula_weight	58879.0 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	4579

ADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH

来源 Source

来源生物 organism	Salmonella typhimurium
NCBI Class编号 ncbi_taxonomy_id	602
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	LYS-DAB-LYS PEPTIDE
Molecular weight formula_weight	376.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

KAK

Entity 3 Entity 3 non-polymer

Description description	URANIUM ATOM
Molecular weight formula_weight	238.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	373

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1b4ha_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

CATH v4.4 (3 domains)

Domain ID domain_id	1b4hA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1b4hA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	76 — Dipeptide-binding Protein; domain 1
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 1

Domain ID domain_id	1b4hA03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	105 — Dipeptide-binding Protein; domain 3
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 3

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8. Citations (2)

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Unit-cell length a length_a	109.722 Å
Unit-cell length b length_b	75.953 Å
Unit-cell length c length_c	70.424 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	4

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1900
R_free r_free	0.2300

fit	/app/data/saxs_computation/b4/1b4h/1b4h.fit
pddf	/app/data/pr_computation/b4/1b4h/1b4h.pr.out
profile	/app/data/saxs_computation/b4/1b4h/1b4h.dat

OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-DIAMINOBUTYRIC ACID-LYSINE

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)