SAXSdb — 1a40

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

PHOSPHATE-BINDING PERIPLASMIC PROTEIN PRECURSOR

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：A197W	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；pH 4.5	Resolution 1.70 Å R-free 0.269

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 1A40	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A55 PHOSPHATE-BINDING PROTEIN MUTANT A197C Deposited 1998-02-19	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–346（321 aa）	Mutation：A197C	2HP DIHYDROGENPHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 2.40 Å R-free 0.227
1IXG PHOSPHATE-BINDING PROTEIN MUTANT WITH THR 141 REPLACED BY ASP (T141D), COMPLEXED WITH PHOSPATE Deposited 1996-08-01	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–346（321 aa）	Mutation：T141D	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 1.05 Å R-free 0.139
1IXH PHOSPHATE-BINDING PROTEIN (PBP) COMPLEXED WITH PHOSPHATE Deposited 1996-08-01	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–346（321 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 0.98 Å R-free 0.141
1IXI PHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 56 REPLACED BY ASN COMPLEX WITH MONOBASIC PHOSPHATE ION Deposited 1996-10-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–346（321 aa）	Mutation：D56N	2HP DIHYDROGENPHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 1.89 Å R-free 0.294
1OIB PHOSPHATE-BINDING PROTEIN MUTANT T141D Deposited 1995-11-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–346（321 aa）	Mutation：T141D	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1OIB PHOSPHATE-BINDING PROTEIN MUTANT T141D Deposited 1995-11-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–346（321 aa）	Mutation：T141D	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1PBP FINE TUNING OF THE SPECIFICITY OF THE PERIPLASMIC PHOSPHATE TRANSPORT RECEPTOR: SITE-DIRECTED MUTAGENESIS, LIGAND BINDING, AND CRYSTALLOGRAPHIC STUDIES Deposited 1994-07-20	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–346（321 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1QUI PHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 137 REPLACED BY GLY COMPLEX WITH BROMINE AND PHOSPHATE Deposited 1995-11-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–346（321 aa）	Mutation：D137G	BR BROMIDE ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.218
1QUJ PHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 137 REPLACED BY GLY COMPLEX WITH CHLORINE AND PHOSPHATE Deposited 1995-11-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–346（321 aa）	Mutation：D137G	CL CHLORIDE ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.209
1QUK PHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 137 REPLACED BY ASN COMPLEX WITH PHOSPHATE Deposited 1995-11-11	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–346（321 aa）	Mutation：D137N	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å R-free 0.189
1QUL PHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 137 REPLACED BY THR COMPLEX WITH CHLORINE AND PHOSPHATE Deposited 1995-11-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–346（321 aa）	Mutation：D137T	PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å R-free 0.205
2ABH PHOSPHATE-BINDING PROTEIN (RE-REFINED) Deposited 1995-11-28	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–346（321 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PSTS_ECOLI
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	1a40
Deposition date deposition_date	1998-02-10
Structure title title	PHOSPHATE-BINDING PROTEIN WITH ALA 197 REPLACED WITH TRP
Keywords keywords	PHOSPHATE-BINDING PROTEIN, MUTAGENESIS, CHARGE COMPLEMENTARY, KINETICS; PHOSPHATE-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	20.79 Å
Radius of gyration Rg (electron density) rg_electron	19.93 Å
Forward intensity I(0) i0	19807400.00
Molecular weight molecular_weight	34615.0 kDa
Excluded volume excluded_volume	43627 Å³
Envelope volume envelope_volume	48876 Å³
Hydration-shell volume shell_volume	20644 Å³
Envelope diameter envelope_diameter	72.6 Å
Shell Rg shell_rg	26.31 Å
Envelope Rg envelope_rg	20.31 Å
Shape Rg shape_rg	19.87 Å
Total Rg total_rg	20.97 Å
Total atoms total_atoms	2451
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	74.0 Å
Rg (real space) rg_real	20.79 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.9810e+07
I(0) uncertainty (real space) i0_real_error	2.7290e+05
Rg (reciprocal space) rg_reciprocal	20.79 Å
I(0) (reciprocal space) i0_reciprocal	19810000.0000
Solution quality estimate total_estimate	0.7577
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.7 Å
Skewness Skewness skewness	0.427
Kurtosis Kurtosis kurtosis	-0.088
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4875000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.623; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PHOSPHATE-BINDING PERIPLASMIC PROTEIN PRECURSOR
Molecular weight formula_weight	34572.7 kDa
Mutation mutation	A197W
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	2862

EASLTGAGATFPAPVYAKWADTYQKETGNKVNYQGIGSSGGVKQIIANTVDFGASDAPLSDEKLAQEGLFQFPTVIGGVVLAVNIPGLKSGELVLDGKTLGDIYLGKIKKWDDEAIAKLNPGLKLPSQNIAVVRRADGSGTSFVFTSYLAKVNEEWKNNVGTGSTVKWPIGLGGKGNDGIAAFVQRLPGAIGYVEYWYAKQNNLAYTKLISADGKPVSPTEENFANAAKGADWSKTFAQDLTNQKGEDAWPITSTTFILIHKDQKKPEQGTEVLKFFDWAYKTGAKQANDLDYASLPDSVVEQVRAAWKTNIKDSSGKPLY

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	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	411

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a40a_
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	1a40A01
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	1a40A02
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 (4)

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Unit-cell length a length_a	41.410 Å
Unit-cell length b length_b	62.760 Å
Unit-cell length c length_c	122.730 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	1.700 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2030
R_work r_work	0.2030
R_free r_free	0.2690

fit	/app/data/saxs_computation/a4/1a40/1a40.fit
pddf	/app/data/pr_computation/a4/1a40/1a40.pr.out
profile	/app/data/saxs_computation/a4/1a40/1a40.dat

PHOSPHATE-BINDING PROTEIN WITH ALA 197 REPLACED WITH TRP

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

PHOSPHATE-BINDING PERIPLASMIC PROTEIN PRECURSOR

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