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3bp3

Crystal structure of EIIB

Method: X-RAY DIFFRACTION Dmax: 57.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glucose-specific phosphotransferase enzyme IIB component

Escherichia coli

UniProt P69786

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 396–477 Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.65 Å R-free 0.241
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 396–477 Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.65 Å R-free 0.241

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 3BP3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IBA GLUCOSE PERMEASE (DOMAIN IIB), NMR, 11 STRUCTURES Deposited 1996-03-23 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 391–476（86 aa） Fragment：DOMAIN IIB
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
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 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 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
3BP8 Crystal structure of Mlc/EIIB complex Deposited 2007-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 8 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 1–82； UniProt 396–477 Author chain B； PDBConstruct 1–82； UniProt 396–477

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3bp3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3bp3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3bp3
Deposition date deposition_date2007-12-18
Structure title titleCrystal structure of EIIB
Keywords keywords;transcription regulation, Inner membrane, Kinase, Membrane, Phosphoprotein, Phosphotransferase system, Sugar transport, Transferase, Transmembrane, Transport ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.20 Å
Radius of gyration Rg (electron density) rg_electron16.27 Å
Forward intensity I(0) i05654010.00
Molecular weight molecular_weight16590.0 kDa
Excluded volume excluded_volume20461 ų
Envelope volume envelope_volume23774 ų
Hydration-shell volume shell_volume12841 ų
Envelope diameter envelope_diameter57.9 Å
Shell Rg shell_rg21.40 Å
Envelope Rg envelope_rg16.56 Å
Shape Rg shape_rg16.24 Å
Total Rg total_rg17.23 Å
Total atoms total_atoms1144
Residues n_residues158
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax57.6 Å
Rg (real space) rg_real17.21 Å
Rg uncertainty (real space) rg_real_error0.35 Å
I(0) (real space) i0_real5.6540e+06
I(0) uncertainty (real space) i0_real_error6.7850e+04
Rg (reciprocal space) rg_reciprocal17.21 Å
I(0) (reciprocal space) i0_reciprocal5654000.0000
Solution quality estimate total_estimate0.7959
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary19.0 Å
Skewness Skewness skewness0.347
Kurtosis Kurtosis kurtosis-0.408
Angular range angular_range— – 0.4650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1568000.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.793; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; 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)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3bp3a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.95 — Homing endonuclease-like
Superfamily Superfamily superfamilyd.95.1 — Glucose permease domain IIB
Family Family familyd.95.1.1 — Glucose permease domain IIB
Domain ID domain_idd3bp3b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.95 — Homing endonuclease-like
Superfamily Superfamily superfamilyd.95.1 — Glucose permease domain IIB
Family Family familyd.95.1.1 — Glucose permease domain IIB

CATH v4.4 (2 domains)

Domain ID domain_id3bp3A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily60 — Glucose permease domain IIB
Domain ID domain_id3bp3B00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily60 — Glucose permease domain IIB
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8. Citations (1)

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9. Files and Curves (10)