SAXSdb — 9wca

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

Peptidyl-prolyl cis-trans isomerase A

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 f； UniProt 1–190 Chain j； UniProt 1–190 Chain z； UniProt 1–190	Not recorded	A8 gpJ 713 × 3	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.49 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	PPIA_ECO57
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain f； PDBConstruct 1–190； UniProt 1–190 Author chain j； PDBConstruct 1–190； UniProt 1–190 Author chain z； PDBConstruct 1–190； UniProt 1–190

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	9wca
Deposition date deposition_date	2025-08-16
Structure title title	Closed state of A8 gpJ 713 central tail fiber
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	49.04 Å
Radius of gyration Rg (electron density) rg_electron	50.27 Å
Forward intensity I(0) i0	366042000.00
Molecular weight molecular_weight	153840.0 kDa
Excluded volume excluded_volume	191460 Å³
Envelope volume envelope_volume	267360 Å³
Hydration-shell volume shell_volume	51159 Å³
Envelope diameter envelope_diameter	215.8 Å
Shell Rg shell_rg	44.28 Å
Envelope Rg envelope_rg	52.30 Å
Shape Rg shape_rg	50.33 Å
Total Rg total_rg	49.81 Å
Total atoms total_atoms	10827
Residues n_residues	1413
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	131.3 Å
Rg (real space) rg_real	45.45 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	3.5200e+08
I(0) uncertainty (real space) i0_real_error	5.7230e+06
Rg (reciprocal space) rg_reciprocal	49.05 Å
I(0) (reciprocal space) i0_reciprocal	365400000.0000
Solution quality estimate total_estimate	0.7063
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	49.3 Å
Skewness Skewness skewness	0.371
Kurtosis Kurtosis kurtosis	-0.593
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0499
Highest regularization parameter α highest_alpha	16650000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.003; Oscil: 0.931; Stabil: 0.975; Sysdev: 0.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.737

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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,Z,F
Atom count atom_count	10827

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	Peptidyl-prolyl cis-trans isomerase A
Molecular weight formula_weight	20453.3 kDa
EC 编号 ec_number	5.2.1.8
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	j,z,f

MFKSTLAAMAAVFALSALSPAAMAAKGDPHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQKKPNPPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSAKVLP

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	3.49 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	861098

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

Closed state of A8 gpJ 713 central tail fiber

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

Peptidyl-prolyl cis-trans isomerase A

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)