SAXSdb — 1pdo

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

MANNOSE PERMEASE

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–132	Fragment：IIA ==MAN== DOMAIN, RESIDUES 2 - 133, OF THE IIAB ==MAN== SUBUNIT PLUS PHE-ALA-GLY AT THE CARBOXY TERMINUS	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.8；pH 6.8	Resolution 1.70 Å R-free 0.244

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 1PDO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1VRC Complex of enzyme IIAmannose and the histidine-containing phosphocarrier protein HPr from escherichia coli nmr, restrained regularized mean structure Deposited 2005-02-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–132（132 aa） Fragment：EIIA DOMAIN Chain B 1–132（132 aa） Fragment：EIIA DOMAIN	Not recorded	PO3 PHOSPHITE ION × 2	SOLUTION NMR NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 40 mM SODIUM PHOSPHATE	Resolution not provided
1VSQ Solution NMR structure of the productive complex between IIAMannose and IIBMannose of the mannose transporter of the E. coli phosphotransferase system Deposited 2008-01-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–134（133 aa） Chain B 2–134（133 aa） Chain C 159–323（165 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 20 mM phosphate；Pressure ambient NMR sample composition 0.5-1 mM IIAMan(H10E)+IIBMan, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-1 mM IIAMan(H10E)+IIBMan, 100% D2O \| 100% D2O	Resolution not provided
2JZH structure of IIB domain of the mannose transporter of E. coli Deposited 2008-01-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 154–323（170 aa） Fragment：PTS EIIB type-4 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 0.5-1 mM [U-100% 13C; U-100% 15N] protein, sodium phosphate, sodium azide, 100% D2O \| 100% D2O NMR sample composition 0.5-1 mM [U-100% 15N] protein, sodium phosphate, sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2JZN Solution NMR structure of the productive complex between IIAMannose and IIBMannose of the mannose transporter of the E. coli phosphotransferase system Deposited 2008-01-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–134（133 aa） Chain B 2–134（133 aa） Chain C 159–323（165 aa）	Mutation：H10E Mutation：H10E	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 20 mM phosphate；Pressure ambient NMR sample composition 0.5-1 mM see details IIAMan(H10E)+IIBMan, 100% D2O \| 100% D2O NMR sample composition 0.5-1 mM see details IIAMan(H10E)+IIBMan, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2JZO Solution NMR structure of the non-productive complex between IIAMannose and IIBMannose of the mannose transporter of the E. coli phosphotransferase system Deposited 2008-01-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–134（133 aa） Fragment：PTS EIIB type-4 domain Chain B 2–134（133 aa） Fragment：PTS EIIB type-4 domain Chain D 159–323（165 aa） Fragment：PTS EIIA type-4 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 20 mM phosphate；Pressure ambient NMR sample composition 0.5-1 mM IIAMan+IIBMan, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-1 mM IIAMan+IIBMan, 100% D2O \| 100% D2O	Resolution not provided

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTNAB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–132； UniProt 1–132

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	1pdo
Deposition date deposition_date	1996-03-08
Structure title title	PHOSPHOENOLPYRUVATE-DEPENDENT PHOSPHOTRANSFERASE SYSTEM
Keywords keywords	PHOSPHOENOLPYRUVATE DEPENDENT PHOSPHOTRANSFERASE SYSTEM, PHOSPHOTRANSFERASE; 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	15.47 Å
Radius of gyration Rg (electron density) rg_electron	14.20 Å
Forward intensity I(0) i0	3739140.00
Molecular weight molecular_weight	14012.0 kDa
Excluded volume excluded_volume	17720 Å³
Envelope volume envelope_volume	20161 Å³
Hydration-shell volume shell_volume	12190 Å³
Envelope diameter envelope_diameter	53.4 Å
Shell Rg shell_rg	19.78 Å
Envelope Rg envelope_rg	14.85 Å
Shape Rg shape_rg	14.18 Å
Total Rg total_rg	15.46 Å
Total atoms total_atoms	988
Residues n_residues	129
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	54.1 Å
Rg (real space) rg_real	15.39 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	3.7390e+06
I(0) uncertainty (real space) i0_real_error	3.9590e+04
Rg (reciprocal space) rg_reciprocal	15.40 Å
I(0) (reciprocal space) i0_reciprocal	3739000.0000
Solution quality estimate total_estimate	0.7651
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.5 Å
Skewness Skewness skewness	0.198
Kurtosis Kurtosis kurtosis	-0.150
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	775300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.652; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1pdoa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.54 — PTS system fructose IIA component-like
Superfamily Superfamily superfamily	c.54.1 — PTS system fructose IIA component-like
Family Family family	c.54.1.1 — EIIA-man component-like

CATH v4.4 (1 domains)

Domain ID domain_id	1pdoA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	510 — Phosphotransferase system, mannose-type IIA component

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8. Citations (2)

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Unit-cell length a length_a	76.360 Å
Unit-cell length b length_b	76.360 Å
Unit-cell length c length_c	88.730 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1890
R_work r_work	0.1890
R_free r_free	0.2440

Description description	MANNOSE PERMEASE
Molecular weight formula_weight	14624.6 kDa
EC 编号 ec_number	2.7.1.69
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1073

PHOSPHOENOLPYRUVATE-DEPENDENT PHOSPHOTRANSFERASE SYSTEM

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

MANNOSE PERMEASE

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

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 K12

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	70

fit	/app/data/saxs_computation/pd/1pdo/1pdo.fit
pddf	/app/data/pr_computation/pd/1pdo/1pdo.pr.out
profile	/app/data/saxs_computation/pd/1pdo/1pdo.dat