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2hdi

Crystal structure of the Colicin I receptor Cir from E.coli in complex with receptor binding domain of Colicin Ia.

Method: X-RAY DIFFRACTION Dmax: 101.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Colicin I receptor

Escherichia coli

UniProt P17315

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 26–663 Fragment：Colicin I receptor Mutation：W338M, L343M, F589M, V591M Colicin-Ia × 1 （P06716） LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.2；294 K；9 G/L PROTEIN IN 0.02M TRIS PH7.5, 0.2M NACL, 0.05% LDAO, 0.45% C8E4, 3% HEPTANETRIOL MIXED AT 1:1 RATIO WITH 0.1M MES PH6.2, 10% GLYCEROL, 22% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 2.50 Å R-free 0.249

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 2HDI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2HDF Crystal structure of the Colicin I receptor Cir from E.coli Deposited 2006-06-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–663（638 aa） Fragment：Colicin I receptor
Mutation：W338M, L343M, F589M, V591M Non-standard monomer：Yes (specific site not provided by mmCIF) SR STRONTIUM ION × 1 OES N-OCTYL-2-HYDROXYETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；7-8 G/L PROTEIN IN 0.02M TRIS PH7.5, 0.001M EDTA, 0.3M NACL, 1% N-OCTYL-2-HYDROXYETHYL SULFOXIDE MIXED AT 1:1 RATIO WITH 0.1M TRIS PH7.5, 0.02-0.05M SRCL2, 5% ISOPROPANOL, 32-40 % PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.65 Å R-free 0.291
9NN6 E. coli Cir in Complex with the RBD of Microcin V Deposited 2025-03-05 Different construct Different mutation/modification 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 32–663（632 aa）
Mutation：W307M, L312M, F558M, V560M No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Phosphate Buffered Saline
cryo-EM vitrification conditions Cryogen ETHANE；Blot force +5 Wait time 0 Blot total 1 Blot time 5 seconds
Resolution 2.90 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CIRA_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–639； UniProt 26–663

Colicin-Ia

Escherichia coli

UniProt P06716

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 282–385 Fragment：R domain of Colicin Ia Colicin I receptor × 1 （P17315） LDA LAURYL DIMETHYLAMINE-N-OXIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.2；294 K；9 G/L PROTEIN IN 0.02M TRIS PH7.5, 0.2M NACL, 0.05% LDAO, 0.45% C8E4, 3% HEPTANETRIOL MIXED AT 1:1 RATIO WITH 0.1M MES PH6.2, 10% GLYCEROL, 22% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 2.50 Å R-free 0.249

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 2HDI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CII COLICIN IA Deposited 1997-01-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–624（602 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions vapor diffusion - hanging drop - streak seeding；pH 5.2；PROTEIN WAS CRYSTALLIZED BY HANGING-DROP VAPOR DIFFUSION AGAINST RESERVOIRS OF 1.0 M NH4(SO4)2, 20 MM NA-CITRATE (PH 5.2), 200 MM NACL, STARTING WITH 6 MICROLITERS OF PROTEIN AT 2 MG/ML IN 20 MM NA-CITRATE (PH 5.2), 200 MM NACL, 5 MM DTT, AND 4 MICROLITERS RESERVOIR SOLUTION. THESE DROPS OF MUTANT PROTEIN WERE STREAK-SEEDED FROM STOCKS GENERATED FROM CRUSHED DIFFRACTION-QUALITY WILD-TYPE COLICIN IA CRYSTALS. CRYSTALS WERE HARVESTED TO 1.1 M NA2SO4, 200 MM NACL, 20 MM NA-CITRATE (PH 5.2), AND 5 MM DTT. FOR DERIVATIZATION, CRYSTALS WERE WASHED IN DTT-FREE HARVEST BUFFER AND SOAKED FOR ONE WEEK IN 1 MM CH3HGCL., vapor diffusion - hanging drop - streak seeding
Resolution 3.00 Å R-free 0.312

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CEIA_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 10–113； UniProt 282–385

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 2hdi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2hdi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2hdi
Deposition date deposition_date2006-06-20
Structure title titleCrystal structure of the Colicin I receptor Cir from E.coli in complex with receptor binding domain of Colicin Ia.
Keywords keywords;Outer membrane, Iron transport, TonB box, Signal transduction, Colicin I Receptor, Receptor Ligand, Membrane Protein, Protein Transport, Antimicrobial Protein ;; Protein Transport,Antimicrobial Protein
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_guinier28.50 Å
Radius of gyration Rg (electron density) rg_electron28.27 Å
Forward intensity I(0) i0104458000.00
Molecular weight molecular_weight78323.0 kDa
Excluded volume excluded_volume97054 ų
Envelope volume envelope_volume122740 ų
Hydration-shell volume shell_volume36885 ų
Envelope diameter envelope_diameter106.8 Å
Shell Rg shell_rg34.97 Å
Envelope Rg envelope_rg28.49 Å
Shape Rg shape_rg28.27 Å
Total Rg total_rg28.88 Å
Total atoms total_atoms5529
Residues n_residues701
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 dmax101.2 Å
Rg (real space) rg_real28.56 Å
Rg uncertainty (real space) rg_real_error0.82 Å
I(0) (real space) i0_real1.0450e+08
I(0) uncertainty (real space) i0_real_error1.5880e+06
Rg (reciprocal space) rg_reciprocal28.54 Å
I(0) (reciprocal space) i0_reciprocal104500000.0000
Solution quality estimate total_estimate0.8347
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.1 Å
Skewness Skewness skewness0.506
Kurtosis Kurtosis kurtosis0.175
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20270000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.638; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.962
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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) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id2hdiA01
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology130 — Ferric Hydroxamate Uptake Protein; Chain A, domain 1
Homologous superfamily homologous superfamily10 — TonB-dependent receptor, plug domain
Domain ID domain_id2hdiA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology170 — Maltoporin; Chain A
Homologous superfamily homologous superfamily20 — TonB-dependent receptor, beta-barrel domain
Domain ID domain_id2hdiB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology305 — Colicin Ia; domain 2
Homologous superfamily homologous superfamily10 — Colicin Ia; domain 2
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8. Citations (1)

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9. Files and Curves (10)