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3bp8

Crystal structure of Mlc/EIIB complex

Method: X-RAY DIFFRACTION Dmax: 111.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Putative NAGC-like transcriptional regulator

Escherichia coli

UniProt Q8X787

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–406 Chain B； UniProt 1–406 Not recorded PTS system glucose-specific EIICB component × 2 （P69786） 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
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–406 Chain B； UniProt 1–406 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q8X787_ECO57
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–406； UniProt 1–406 Author chain B； PDBConstruct 1–406； UniProt 1–406

PTS system glucose-specific EIICB 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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 401–475 Chain D； UniProt 401–475 Fragment：UNP residues 401-475 Putative NAGC-like transcriptional regulator × 2 （Q8X787） 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 401–475 Fragment：UNP residues 401-475 No other associated polymer 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
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 401–475 Fragment：UNP residues 401-475 No other associated polymer 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

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 3BP8 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 experimental method Different experimental conditions 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 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
3BP3 Crystal structure of EIIB Deposited 2007-12-18 Different construct 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 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 conditions 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
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 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 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 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 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PTGCB_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–75； UniProt 401–475 Author chain D； PDBConstruct 1–75； UniProt 401–475

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 3bp8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3bp8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3bp8
Deposition date deposition_date2007-12-18
Structure title titleCrystal structure of Mlc/EIIB complex
Keywords keywords;enzyme, IICBGlc, glucose signaling, Mlc, protein-protein interaction, transcription regulation, Inner membrane, Kinase, Membrane, Phosphoprotein, Phosphotransferase system, Sugar transport, Transferase, Transmembrane, Transport, TRANSCRIPTION ;; TRANSCRIPTION
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_guinier33.20 Å
Radius of gyration Rg (electron density) rg_electron32.63 Å
Forward intensity I(0) i0151897000.00
Molecular weight molecular_weight98968.0 kDa
Excluded volume excluded_volume124430 ų
Envelope volume envelope_volume159980 ų
Hydration-shell volume shell_volume41434 ų
Envelope diameter envelope_diameter115.7 Å
Shell Rg shell_rg38.78 Å
Envelope Rg envelope_rg32.64 Å
Shape Rg shape_rg32.61 Å
Total Rg total_rg33.18 Å
Total atoms total_atoms6943
Residues n_residues911
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 dmax111.3 Å
Rg (real space) rg_real33.21 Å
Rg uncertainty (real space) rg_real_error1.10 Å
I(0) (real space) i0_real1.5190e+08
I(0) uncertainty (real space) i0_real_error2.7950e+06
Rg (reciprocal space) rg_reciprocal33.21 Å
I(0) (reciprocal space) i0_reciprocal151900000.0000
Solution quality estimate total_estimate0.8146
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.1 Å
Skewness Skewness skewness0.344
Kurtosis Kurtosis kurtosis-0.368
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28640000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.871; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd3bp8a1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.63 — ROK associated domain
Domain ID domain_idd3bp8a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.10 — ROK
Domain ID domain_idd3bp8a3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.10 — ROK
Domain ID domain_idd3bp8b1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.5 — 'Winged helix' DNA-binding domain
Family Family familya.4.5.63 — ROK associated domain
Domain ID domain_idd3bp8b2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.10 — ROK
Domain ID domain_idd3bp8b3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.10 — ROK
Domain ID domain_idd3bp8c_
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_idd3bp8d_
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 (8 domains)

Domain ID domain_id3bp8A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id3bp8A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id3bp8A03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id3bp8B01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id3bp8B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id3bp8B03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id3bp8C00
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_id3bp8D00
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)