SAXSdb — 9wcb

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

Outer membrane porin C

Escherichia coli O157:H7 str. EDL933

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 22–367 Chain B； UniProt 22–367 Chain C； UniProt 22–367	Not recorded	A8 gpJ 713 × 3	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.89 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	OMPC_ECO57
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–346； UniProt 22–367 Author chain B； PDBConstruct 1–346； UniProt 22–367 Author chain C； PDBConstruct 1–346； UniProt 22–367

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	9wcb
Deposition date deposition_date	2025-08-16
Structure title title	Open state of A8 gpJ 713 central tail fiber with OmpC G17 from E. coli EDL933
Keywords keywords	Phage Tail, VIRAL PROTEIN; VIRAL 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	36.99 Å
Radius of gyration Rg (electron density) rg_electron	36.97 Å
Forward intensity I(0) i0	485402000.00
Molecular weight molecular_weight	171620.0 kDa
Excluded volume excluded_volume	211310 Å³
Envelope volume envelope_volume	269480 Å³
Hydration-shell volume shell_volume	60470 Å³
Envelope diameter envelope_diameter	133.1 Å
Shell Rg shell_rg	43.30 Å
Envelope Rg envelope_rg	37.22 Å
Shape Rg shape_rg	36.93 Å
Total Rg total_rg	37.47 Å
Total atoms total_atoms	12120
Residues n_residues	1560
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	125.7 Å
Rg (real space) rg_real	37.09 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	4.8540e+08
I(0) uncertainty (real space) i0_real_error	8.5980e+06
Rg (reciprocal space) rg_reciprocal	37.03 Å
I(0) (reciprocal space) i0_reciprocal	485400000.0000
Solution quality estimate total_estimate	0.8430
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.9 Å
Skewness Skewness skewness	0.544
Kurtosis Kurtosis kurtosis	0.178
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	101700000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.743; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.738

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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	A8 gpJ 713
Molecular weight formula_weight	47315.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,F,Z
Atom count atom_count	12120

HHHHHHHHAPAAPSRIELTPGYFQITATPHLAVYDPTVQFEFWFSEKQIADIRQVETSTRYLGTALYWIAASINIKPGHDYYFYIRSVNTVGKSAFVEAVGRASDDAEGYLDFFKGKITESHLGKELLEKVELTEDNASRLEEFSKEWKDASDKWNAMWAVKIEQTKDGKHYVAGIGLSMEDTEEGKLSQFLVAANRIAFIDPANGNETPMFVAQGNQIFMNDVFLKRLTAPTITSGGNPPAFSLTPDGKLTAKNADISGSVNANSGTLNNVTINENCQIKGKLSANQIEGDIVKTVSKSFPRTNSYASGTITVRISDDQKFDRQVMIPPVLFRGGKHENFNSNNQQSYWYSTCRLRVTRNGQEIFNQSTTDAQGVFSSVIDMPAGQGTLTLTFTVSSSGANNWTPTTSISDLLVVVMKKSTAGISIS

来源 Source

来源生物 organism	Escherichia phage Lambda
NCBI Class编号 ncbi_taxonomy_id	2681611
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Outer membrane porin C
Molecular weight formula_weight	38476.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C

AEVYNKDGNKLDLYGKVDGLHYFSDDKSVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQIQGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFMQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKNGSVSGEGMTNNGREALRQNGDGVGGSITYDYEGFGIGAAVSSSKRTDDQNSPLYIGNGDRAETYTGGLKYDANNIYLAAQYTQTYNATRVGSLGWANKAQNFEAVAQYQFDFGLRPSLAYLQSKGKNLGVINGRNYDDEDILKYVDVGATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF

来源 Source

来源生物 organism	Escherichia coli O157:H7 str. EDL933
NCBI Class编号 ncbi_taxonomy_id	155864
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	3.89 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	168284

fit	/app/data/saxs_computation/wc/9wcb/9wcb.fit
pddf	/app/data/pr_computation/wc/9wcb/9wcb.pr.out
profile	/app/data/saxs_computation/wc/9wcb/9wcb.dat

Open state of A8 gpJ 713 central tail fiber with OmpC G17 from E. coli EDL933

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

Outer membrane porin C

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

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)