SAXSdb — 1a3a

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

MANNITOL-SPECIFIC EII

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 491–637 Chain C； UniProt 491–637	Fragment：IIA DOMAIN, RESIDUES 491 - 637	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 1.80 Å R-free 0.242
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 491–637 Chain D； UniProt 491–637	Fragment：IIA DOMAIN, RESIDUES 491 - 637	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 1.80 Å R-free 0.242

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 1A3A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1J6T COMPLEX OF ENZYME IIAMTL AND THE HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR FROM ESCHERICHIA COLI NMR, RESTRAINED REGULARIZED MEAN STRUCTURE Deposited 2002-08-14	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 × 2 PDB declaration: dimeric	Chain A 491–637（147 aa） Fragment：EIIA DOMAIN	Not recorded	PO3 PHOSPHITE ION × 1	SOLUTION NMR NMR measurement conditions pH 7；308 K；Ionic strength (raw mmCIF value) 10 mM SODIUM PHOSPHATE	Resolution not provided
1VKR STRUCTURE OF IIB DOMAIN OF THE MANNITOL-SPECIFIC PERMEASE ENZYME II Deposited 2004-06-14	Different construct Different mutation/modification 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 367–489（123 aa） Fragment：IIB DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.1；308 K；Ionic strength (raw mmCIF value) 40 mM SODIUM PHOSPHATE	Resolution not provided
1VRV Structure of phosphorylated IIB (C384(SEP)) domain of the mannitol-specific permease enzyme II Deposited 2005-06-17	Different construct Different mutation/modification 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 375–475（101 aa） Fragment：IIB DOMAIN	Mutation：C384(SEP) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0 EXCEPT FOR RDC MEASUREMENTS IN PHAGE PF1 WHERE IT WAS 0.5M	Resolution not provided
2FEW Complex of enzyme IIAMTL and phosphorylated enzyme IIBMTL from Escherichia coli NMR, restrained regularized mean structure Deposited 2005-12-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 491–637（147 aa） Fragment：EIIA-MTL, PHOSPHOTRANSFERASE ENZYME II, A DOMAIN COMPONENT	Mutation：H65Q	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 20 mM TRIS-D11	Resolution not provided

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTM3C_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–148； UniProt 491–637 Author chain B； PDBConstruct 2–148； UniProt 491–637 Author chain C； PDBConstruct 2–148； UniProt 491–637 Author chain D； PDBConstruct 2–148； UniProt 491–637

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	1a3a
Deposition date deposition_date	1998-01-19
Structure title title	CRYSTAL STRUCTURE OF IIA MANNITOL FROM ESCHERICHIA COLI
Keywords keywords	PHOSPHOENOLPYRUVATE DEPENDENT PHOSPHOTRANSFERASE SYSTEM, IIA ENZYMES, HISTIDINE PHOSPHORYLATION, 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	31.27 Å
Radius of gyration Rg (electron density) rg_electron	30.85 Å
Forward intensity I(0) i0	63949900.00
Molecular weight molecular_weight	63452.0 kDa
Excluded volume excluded_volume	79658 Å³
Envelope volume envelope_volume	101040 Å³
Hydration-shell volume shell_volume	27871 Å³
Envelope diameter envelope_diameter	102.5 Å
Shell Rg shell_rg	36.89 Å
Envelope Rg envelope_rg	30.50 Å
Shape Rg shape_rg	30.84 Å
Total Rg total_rg	31.43 Å
Total atoms total_atoms	4473
Residues n_residues	576
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	100.9 Å
Rg (real space) rg_real	31.41 Å
Rg uncertainty (real space) rg_real_error	0.94 Å
I(0) (real space) i0_real	6.3950e+07
I(0) uncertainty (real space) i0_real_error	9.8210e+05
Rg (reciprocal space) rg_reciprocal	31.35 Å
I(0) (reciprocal space) i0_reciprocal	63950000.0000
Solution quality estimate total_estimate	0.8682
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	25.7 Å
Skewness Skewness skewness	0.342
Kurtosis Kurtosis kurtosis	-0.698
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16290000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.793; Smooth: 0.883

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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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1a3aa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.112 — Phoshotransferase/anion transport protein
Superfamily Superfamily superfamily	d.112.1 — Phoshotransferase/anion transport protein
Family Family family	d.112.1.1 — IIA domain of mannitol-specific and ntr phosphotransferase EII

Domain ID domain_id	d1a3ab_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.112 — Phoshotransferase/anion transport protein
Superfamily Superfamily superfamily	d.112.1 — Phoshotransferase/anion transport protein
Family Family family	d.112.1.1 — IIA domain of mannitol-specific and ntr phosphotransferase EII

Domain ID domain_id	d1a3ac_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.112 — Phoshotransferase/anion transport protein
Superfamily Superfamily superfamily	d.112.1 — Phoshotransferase/anion transport protein
Family Family family	d.112.1.1 — IIA domain of mannitol-specific and ntr phosphotransferase EII

Domain ID domain_id	d1a3ad_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.112 — Phoshotransferase/anion transport protein
Superfamily Superfamily superfamily	d.112.1 — Phoshotransferase/anion transport protein
Family Family family	d.112.1.1 — IIA domain of mannitol-specific and ntr phosphotransferase EII

CATH v4.4 (4 domains)

Domain ID domain_id	1a3aA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	930 — Mannitol-specific EII; Chain A
Homologous superfamily homologous superfamily	10 — Mannitol-specific EII; Chain A

Domain ID domain_id	1a3aB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	930 — Mannitol-specific EII; Chain A
Homologous superfamily homologous superfamily	10 — Mannitol-specific EII; Chain A

Domain ID domain_id	1a3aC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	930 — Mannitol-specific EII; Chain A
Homologous superfamily homologous superfamily	10 — Mannitol-specific EII; Chain A

Domain ID domain_id	1a3aD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	930 — Mannitol-specific EII; Chain A
Homologous superfamily homologous superfamily	10 — Mannitol-specific EII; Chain A

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8. Citations (1)

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Unit-cell length a length_a	53.570 Å
Unit-cell length b length_b	66.010 Å
Unit-cell length c length_c	73.860 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.76 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	5.000 Å
R factor r_factor	0.1900
R_work r_work	0.1900
R_free r_free	0.2420

Description description	MANNITOL-SPECIFIC EII
Molecular weight formula_weight	16348.5 kDa
EC 编号 ec_number	2.7.1.69
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5041

CRYSTAL STRUCTURE OF IIA MANNITOL FROM ESCHERICHIA COLI

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

MANNITOL-SPECIFIC EII

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	568

fit	/app/data/saxs_computation/a3/1a3a/1a3a.fit
pddf	/app/data/pr_computation/a3/1a3a/1a3a.pr.out
profile	/app/data/saxs_computation/a3/1a3a/1a3a.dat