SAXSdb — 1a54

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

Phosphate-binding protein PstS

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 26–346	Mutation：A197C	2HP DIHYDROGENPHOSPHATE ION × 1 MDC N-[2-(1-MALEIMIDYL)ETHYL]-7-DIETHYLAMINOCOUMARIN-3-CARBOXAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；pH 4.5	Resolution 1.60 Å R-free 0.208

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	A0A4S1QQS5_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–321； UniProt 26–346

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	1a54
Deposition date deposition_date	1998-02-19
Structure title title	PHOSPHATE-BINDING PROTEIN MUTANT A197C LABELLED WITH A COUMARIN FLUOROPHORE AND BOUND TO DIHYDROGENPHOSPHATE ION
Keywords keywords	PHOSPHOTRANSFERASE, TRANSPORT, COUMARIN, FLUOROPHORE; PHOSPHOTRANSFERASE
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	20.85 Å
Radius of gyration Rg (electron density) rg_electron	19.91 Å
Forward intensity I(0) i0	20291200.00
Molecular weight molecular_weight	34645.0 kDa
Excluded volume excluded_volume	43523 Å³
Envelope volume envelope_volume	49251 Å³
Hydration-shell volume shell_volume	20790 Å³
Envelope diameter envelope_diameter	72.8 Å
Shell Rg shell_rg	26.30 Å
Envelope Rg envelope_rg	20.29 Å
Shape Rg shape_rg	19.86 Å
Total Rg total_rg	20.93 Å
Total atoms total_atoms	2452
Residues n_residues	321
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	70.1 Å
Rg (real space) rg_real	20.85 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	2.0290e+07
I(0) uncertainty (real space) i0_real_error	2.8510e+05
Rg (reciprocal space) rg_reciprocal	20.85 Å
I(0) (reciprocal space) i0_reciprocal	20290000.0000
Solution quality estimate total_estimate	0.5893
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.4 Å
Skewness Skewness skewness	0.424
Kurtosis Kurtosis kurtosis	-0.090
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5038000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.710; Stabil: 1.000; Sysdev: 0.177; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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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	Phosphate-binding protein PstS
Molecular weight formula_weight	34489.7 kDa
Mutation mutation	A197C
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	2817

EASLTGAGATFPAPVYAKWADTYQKETGNKVNYQGIGSSGGVKQIIANTVDFGASDAPLSDEKLAQEGLFQFPTVIGGVVLAVNIPGLKSGELVLDGKTLGDIYLGKIKKWDDEAIAKLNPGLKLPSQNIAVVRRADGSGTSFVFTSYLAKVNEEWKNNVGTGSTVKWPIGLGGKGNDGIAAFVQRLPGAIGYVEYCYAKQNNLAYTKLISADGKPVSPTEENFANAAKGADWSKTFAQDLTNQKGEDAWPITSTTFILIHKDQKKPEQGTEVLKFFDWAYKTGAKQANDLDYASLPDSVVEQVRAAWKTNIKDSSGKPLY

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DIHYDROGENPHOSPHATE ION
Molecular weight formula_weight	97.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	N-[2-(1-MALEIMIDYL)ETHYL]-7-DIETHYLAMINOCOUMARIN-3-CARBOXAMIDE
Molecular weight formula_weight	383.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	334

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a54a_
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 (2 domains)

Domain ID domain_id	1a54A01
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	1a54A02
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

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8. Citations (2)

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Unit-cell length a length_a	41.498 Å
Unit-cell length b length_b	62.651 Å
Unit-cell length c length_c	122.608 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	1.600 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	—
R_work r_work	0.1770
R_free r_free	0.2080

fit	/app/data/saxs_computation/a5/1a54/1a54.fit
pddf	/app/data/pr_computation/a5/1a54/1a54.pr.out
profile	/app/data/saxs_computation/a5/1a54/1a54.dat

PHOSPHATE-BINDING PROTEIN MUTANT A197C LABELLED WITH A COUMARIN FLUOROPHORE AND BOUND TO DIHYDROGENPHOSPHATE ION

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

Phosphate-binding protein PstS

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