SAXSdb — 1iba

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

GLUCOSE 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 391–476	Fragment：DOMAIN IIB	No other associated polymer	SOLUTION NMR mmCIF provides none of the parsed experimental conditions	Resolution not provided

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 1IBA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1O2F COMPLEX OF ENZYME IIAGLC AND IIBGLC PHOSPHOCARRIER PROTEIN HPR FROM ESCHERICHIA COLI NMR, RESTRAINED REGULARIZED MEAN STRUCTURE Deposited 2003-03-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 387–476（90 aa）	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
3BP3 Crystal structure of EIIB Deposited 2007-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 396–477（82 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.65 Å R-free 0.241
3BP3 Crystal structure of EIIB Deposited 2007-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 396–477（82 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.65 Å R-free 0.241
3BP8 Crystal structure of Mlc/EIIB complex Deposited 2007-12-18	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 C 401–475（75 aa） Fragment：UNP residues 401-475 Chain D 401–475（75 aa） Fragment：UNP residues 401-475	Not recorded	ACT ACETATE ION × 3 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；6% PEG 6K, 0.1M MgCl2, 0.1M sodium acetate, pH5.5	Resolution 2.85 Å R-free 0.301
3BP8 Crystal structure of Mlc/EIIB complex Deposited 2007-12-18	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 401–475（75 aa） Fragment：UNP residues 401-475	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；6% PEG 6K, 0.1M MgCl2, 0.1M sodium acetate, pH5.5	Resolution 2.85 Å R-free 0.301
3BP8 Crystal structure of Mlc/EIIB complex Deposited 2007-12-18	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 401–475（75 aa） Fragment：UNP residues 401-475	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；6% PEG 6K, 0.1M MgCl2, 0.1M sodium acetate, pH5.5	Resolution 2.85 Å R-free 0.301
8QSR Cryo-EM structure of the glucose-specific PTS transporter IICB from E. coli in the inward-facing conformation Deposited 2023-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–477（477 aa） Chain B 1–477（477 aa）	Not recorded	BGC beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.56 Å
8QST Cryo-EM structure of the glucose-specific PTS transporter IICB from E. coli in the inward- and outward-facing conformation Deposited 2023-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–477（477 aa） Chain B 1–477（477 aa）	Not recorded	BGC beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å
9HNP Cryo-EM structure of the glucose-specific PTS transporter IICB from E. coli in an intermediate state Deposited 2024-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–477（477 aa） Chain B 1–477（477 aa）	Not recorded	LMT DODECYL-BETA-D-MALTOSIDE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTGCB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–90； UniProt 391–476

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	1iba
Deposition date deposition_date	1996-03-23
Structure title title	GLUCOSE PERMEASE (DOMAIN IIB), NMR, 11 STRUCTURES
Keywords keywords	PHOSPHOTRANSFERASE SYSTEM, SUGAR TRANSPORT, TRANSFERASE, PHOSPHORYLATION, TRANSMEMBRANE, INNER MEMBRANE, PHOSPHOTRANSFERASE; PHOSPHOTRANSFERASE
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	12.57 Å
Radius of gyration Rg (electron density) rg_electron	12.10 Å
Forward intensity I(0) i0	112305000.00
Molecular weight molecular_weight	88597.0 kDa
Excluded volume excluded_volume	111280 Å³
Envelope volume envelope_volume	16613 Å³
Hydration-shell volume shell_volume	10847 Å³
Envelope diameter envelope_diameter	44.0 Å
Shell Rg shell_rg	18.71 Å
Envelope Rg envelope_rg	13.41 Å
Shape Rg shape_rg	12.08 Å
Total Rg total_rg	12.43 Å
Total atoms total_atoms	12604
Residues n_residues	858
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	40.5 Å
Rg (real space) rg_real	12.52 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	1.1230e+08
I(0) uncertainty (real space) i0_real_error	1.0560e+06
Rg (reciprocal space) rg_reciprocal	12.52 Å
I(0) (reciprocal space) i0_reciprocal	112300000.0000
Solution quality estimate total_estimate	0.8224
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.9 Å
Skewness Skewness skewness	0.087
Kurtosis Kurtosis kurtosis	-0.448
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	65550.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ibaa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.95 — Homing endonuclease-like
Superfamily Superfamily superfamily	d.95.1 — Glucose permease domain IIB
Family Family family	d.95.1.1 — Glucose permease domain IIB

Domain ID domain_id	d1ibaa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1ibaA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	60 — Glucose permease domain IIB

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8. Citations (5)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	GLUCOSE PERMEASE
Molecular weight formula_weight	10752.1 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	12604

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

GLUCOSE PERMEASE (DOMAIN IIB), NMR, 11 STRUCTURES

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

GLUCOSE 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (5)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/ib/1iba/1iba.fit
pddf	/app/data/pr_computation/ib/1iba/1iba.pr.out
profile	/app/data/saxs_computation/ib/1iba/1iba.dat