SAXSdb — 2hdf

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

Colicin I receptor

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 26–663	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

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 2HDF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2HDI Crystal structure of the Colicin I receptor Cir from E.coli in complex with receptor binding domain of Colicin Ia. Deposited 2006-06-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–663（638 aa） Fragment：Colicin I receptor	Mutation：W338M, L343M, F589M, V591M	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
9NN6 E. coli Cir in Complex with the RBD of Microcin V Deposited 2025-03-05	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 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

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	2hdf
Deposition date deposition_date	2006-06-20
Structure title title	Crystal structure of the Colicin I receptor Cir from E.coli
Keywords keywords	Outer membrane, Iron transport, TonB box, Signal transduction, Colicin I Receptor, Membrane Protein, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	25.31 Å
Radius of gyration Rg (electron density) rg_electron	24.47 Å
Forward intensity I(0) i0	74699000.00
Molecular weight molecular_weight	64576.0 kDa
Excluded volume excluded_volume	79368 Å³
Envelope volume envelope_volume	103440 Å³
Hydration-shell volume shell_volume	34173 Å³
Envelope diameter envelope_diameter	82.6 Å
Shell Rg shell_rg	32.81 Å
Envelope Rg envelope_rg	24.43 Å
Shape Rg shape_rg	24.50 Å
Total Rg total_rg	25.32 Å
Total atoms total_atoms	4520
Residues n_residues	574
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	79.7 Å
Rg (real space) rg_real	25.13 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	7.4700e+07
I(0) uncertainty (real space) i0_real_error	9.2710e+05
Rg (reciprocal space) rg_reciprocal	25.19 Å
I(0) (reciprocal space) i0_reciprocal	74700000.0000
Solution quality estimate total_estimate	0.8844
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.2 Å
Skewness Skewness skewness	0.100
Kurtosis Kurtosis kurtosis	-0.376
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12060000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.961

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Colicin I receptor
Molecular weight formula_weight	71763.2 kDa
Mutation mutation	W338M, L343M, F589M, V591M
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4558

SVDDDGETMVVTASSVEQNLKDAPASISVITQEDLQRKPVQNLKDVLKEVPGVQLTNEGDNRKGVSIRGLDSSYTLILVDGKRVNSRNAVFRHNDFDLNWIPVDSIERIEVVRGPMSSLYGSDALGGVVNIITKKIGQKWSGTVTVDTTIQEHRDRGDTYNGQFFTSGPLIDGVLGMKAYGSLAKREKDDPQNSTTTDTGETPRIEGFSSRDGNVEFAWTPNQNHDFTAGYGFDRQDRDSDSLDKNRLERQNYSVSHNGRWDYGTSELKYYGEKVENKNPGNSSPITSESNTVDGKYTLPLTAINQFLTVGGEMRHDKMSDAVNLTGGTSSKTSASQYALFVEDEWRIFEPLALTTGVRMDDHETYGEHWSPRAYLVYNATDTVTVKGGWATAFKAPSLLQLSPDWTSNSCRGACKIVGSPDLKPETSESWELGLYYMGEEGWLEGVESSVTVFRNDVKDRISISRTSDVNAAPGYQNFVGFETGANGRRIPVFSYYNVNKARIQGVETELKIPFNDEWKLSINYTYNDGRDVSNGENKPLSDLPFHTANGTLDWKPLALEDWSMYMSGHYTGQKRADSATAKTPGGYTIWNTGAAWQVTKDVKLRAGVLNLGDKDLSRDDYSYNEDGRRYFMAVDYRF

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	STRONTIUM ION
Molecular weight formula_weight	87.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	N-OCTYL-2-HYDROXYETHYL SULFOXIDE
Molecular weight formula_weight	206.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	18

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2hdfA01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	130 — Ferric Hydroxamate Uptake Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — TonB-dependent receptor, plug domain

Domain ID domain_id	2hdfA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	170 — Maltoporin; Chain A
Homologous superfamily homologous superfamily	20 — TonB-dependent receptor, beta-barrel domain

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8. Citations (1)

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Unit-cell length a length_a	90.593 Å
Unit-cell length b length_b	84.336 Å
Unit-cell length c length_c	99.458 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.16 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2414
R_work r_work	0.2387
R_free r_free	0.2911

fit	/app/data/saxs_computation/hd/2hdf/2hdf.fit
pddf	/app/data/pr_computation/hd/2hdf/2hdf.pr.out
profile	/app/data/saxs_computation/hd/2hdf/2hdf.dat

Crystal structure of the Colicin I receptor Cir from E.coli

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

Colicin I receptor

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