SAXSdb — 9nn6

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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 32–663	Mutation：W307M, L312M, F558M, V560M	Colicin-V × 1 （P22522）	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

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 9NN6	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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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
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 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 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

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 1–632； UniProt 32–663

Colicin-V

Enterobacteriaceae

UniProt P22522

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 72–103	Not recorded	Colicin I receptor × 1 （P17315）	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

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	CEAV_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–32； UniProt 72–103

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	9nn6
Deposition date deposition_date	2025-03-05
Structure title title	E. coli Cir in Complex with the RBD of Microcin V
Keywords keywords	TonB-dependent receptor, beta barrel, antimicrobial protein, MccV, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	25.94 Å
Radius of gyration Rg (electron density) rg_electron	25.20 Å
Forward intensity I(0) i0	96094700.00
Molecular weight molecular_weight	74043.0 kDa
Excluded volume excluded_volume	91348 Å³
Envelope volume envelope_volume	114060 Å³
Hydration-shell volume shell_volume	36372 Å³
Envelope diameter envelope_diameter	87.2 Å
Shell Rg shell_rg	33.96 Å
Envelope Rg envelope_rg	25.36 Å
Shape Rg shape_rg	25.22 Å
Total Rg total_rg	26.02 Å
Total atoms total_atoms	5224
Residues n_residues	664
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	82.9 Å
Rg (real space) rg_real	25.79 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	9.6090e+07
I(0) uncertainty (real space) i0_real_error	1.4100e+06
Rg (reciprocal space) rg_reciprocal	25.83 Å
I(0) (reciprocal space) i0_reciprocal	96100000.0000
Solution quality estimate total_estimate	0.8805
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.0 Å
Skewness Skewness skewness	0.192
Kurtosis Kurtosis kurtosis	-0.301
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22580000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.944

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Colicin I receptor
Molecular weight formula_weight	70576.6 kDa
Mutation mutation	W307M, L312M, F558M, V560M
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	5224

TMVVTASSVEQNLKDAPASISVITQEDLQRKPVQNLKDVLKEVPGVQLTNEGDNRKGVSIRGLDSSYTLILVDGKRVNSRNAVFRHNDFDLNWIPVDSIERIEVVRGPMSSLYGSDALGGVVNIITKKIGQKWSGTVTVDTTIQEHRDRGDTYNGQFFTSGPLIDGVLGMKAYGSLAKREKDDPQNSTTTDTGETPRIEGFSSRDGNVEFAWTPNQNHDFTAGYGFDRQDRDSDSLDKNRLERQNYSVSHNGRWDYGTSELKYYGEKVENKNPGNSSPITSESNTVDGKYTLPLTAINQFLTVGGEMRHDKMSDAVNLTGGTSSKTSASQYALFVEDEWRIFEPLALTTGVRMDDHETYGEHWSPRAYLVYNATDTVTVKGGWATAFKAPSLLQLSPDWTSNSCRGACKIVGSPDLKPETSESWELGLYYMGEEGWLEGVESSVTVFRNDVKDRISISRTSDVNAAPGYQNFVGFETGANGRRIPVFSYYNVNKARIQGVETELKIPFNDEWKLSINYTYNDGRDVSNGENKPLSDLPFHTANGTLDWKPLALEDWSMYMSGHYTGQKRADSATAKTPGGYTIWNTGAAWQVTKDVKLRAGVLNLGDKDLSRDDYSYNEDGRRYFMAVDYRF

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 polymer

Description description	Colicin-V
Molecular weight formula_weight	3565.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

KQKPEGIPSEAWNYAAGRLCNWSPNNLSDVCL

来源 Source

来源生物 organism	Enterobacteriaceae
NCBI Class编号 ncbi_taxonomy_id	543
宿主生物 host_organism	Escherichia coli BL21(DE3)

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8. Citations (1)

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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	—

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

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.90 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	102419

fit	/app/data/saxs_computation/nn/9nn6/9nn6.fit
pddf	/app/data/pr_computation/nn/9nn6/9nn6.pr.out
profile	/app/data/saxs_computation/nn/9nn6/9nn6.dat

E. coli Cir in Complex with the RBD of Microcin V

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

Colicin-V

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)