10yy

Crystal Structure of the Chaperonin GroEL apical domain from Bordetella pertussis

Method: X-RAY DIFFRACTION D_max: 59.8 Å Quality: GOOD

▼

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

Chaperonin GroEL

Bordetella pertussis Tohama I

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 192–374	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；JCSG+ D12: 0.04M Potassium phosphate monobasic, 16% PEG 6000. plate 20567 D12 drop 1, Puck: PSL-1601, Cryo: 80% crystallant + 20% glycerol	Resolution 2.95 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CH60_BORPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–191； UniProt 192–374

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	10yy
Deposition date deposition_date	2026-02-12
最后修订 last_revision	2026-02-25
Structure title title	Crystal Structure of the Chaperonin GroEL apical domain from Bordetella pertussis
Keywords keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, Chaperonin, GroEL, CHAPERONE; CHAPERONE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	17.63 Å
Radius of gyration Rg (electron density) rg_electron	16.34 Å
Forward intensity I(0) i0	7343290.00
Molecular weight molecular_weight	19648.0 kDa
Excluded volume excluded_volume	24634 Å³
Envelope volume envelope_volume	28461 Å³
Hydration-shell volume shell_volume	14958 Å³
Envelope diameter envelope_diameter	59.4 Å
Shell Rg shell_rg	22.06 Å
Envelope Rg envelope_rg	16.70 Å
Shape Rg shape_rg	16.34 Å
Total Rg total_rg	17.36 Å
Total atoms total_atoms	1380
Residues n_residues	184
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	59.8 Å
Rg (real space) rg_real	17.57 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	7.3430e+06
I(0) uncertainty (real space) i0_real_error	9.6230e+04
Rg (reciprocal space) rg_reciprocal	17.58 Å
I(0) (reciprocal space) i0_reciprocal	7343000.0000
Solution quality estimate total_estimate	0.7786
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.1 Å
Skewness Skewness skewness	0.298
Kurtosis Kurtosis kurtosis	-0.154
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1523000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.711; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

Unit-cell length a length_a	145.768 Å
Unit-cell length b length_b	145.768 Å
Unit-cell length c length_c	34.858 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	47.710 Å
R factor r_factor	0.2148
R_work r_work	0.2129
R_free r_free	0.2490

Description description	Chaperonin GroEL
Molecular weight formula_weight	21058.0 kDa
EC 编号 ec_number	5.6.1.7
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1380

Crystal Structure of the Chaperonin GroEL apical domain from Bordetella pertussis

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

Chaperonin GroEL

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Bordetella pertussis Tohama I
NCBI Class编号 ncbi_taxonomy_id	257313
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/0y/10yy/10yy.fit
pddf	/app/data/pr_computation/0y/10yy/10yy.pr.out
profile	/app/data/saxs_computation/0y/10yy/10yy.dat