SAXSdb — 9yah

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

Copper chaperone PCu(A)C

Neisseria meningitidis serogroup A

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 1–157	Not recorded	CU COPPER (II) ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；296 K；0.2 M NaCl, 25% w/v PEG3350, 0.1 M Tris (pH 8.5)	Resolution 2.90 Å R-free 0.271

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	Q9JYJ5_NEIMB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–157； UniProt 1–157

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	9yah
Deposition date deposition_date	2025-09-15
Structure title title	Crystal structure of metallochaperone AccA from Neisseria gonorrhoeae
Keywords keywords	Metallochaperone, Metal binding protein; METAL BINDING PROTEIN
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	15.56 Å
Radius of gyration Rg (electron density) rg_electron	14.33 Å
Forward intensity I(0) i0	3708970.00
Molecular weight molecular_weight	13484.0 kDa
Excluded volume excluded_volume	16836 Å³
Envelope volume envelope_volume	19123 Å³
Hydration-shell volume shell_volume	11698 Å³
Envelope diameter envelope_diameter	52.5 Å
Shell Rg shell_rg	19.59 Å
Envelope Rg envelope_rg	14.72 Å
Shape Rg shape_rg	14.31 Å
Total Rg total_rg	15.47 Å
Total atoms total_atoms	938
Residues n_residues	121
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	54.3 Å
Rg (real space) rg_real	15.50 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	3.7090e+06
I(0) uncertainty (real space) i0_real_error	4.2540e+04
Rg (reciprocal space) rg_reciprocal	15.51 Å
I(0) (reciprocal space) i0_reciprocal	3709000.0000
Solution quality estimate total_estimate	0.8676
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.2 Å
Skewness Skewness skewness	0.206
Kurtosis Kurtosis kurtosis	-0.366
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	507400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.766; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Copper chaperone PCu(A)C
Molecular weight formula_weight	17006.8 kDa
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	938

MKKLLAAVMMAGLAGAVSAAGVHVEDGWARTTVEGMKIGGAFMKIHNDEAKQDFLLGGSSPVADRVEVHTHINDNGVMRMREVEGGVPLEAKSVTELKPGSYHVMFMGLKKQLKEGDKIPVTLKFKNAKAQTVQLEVKIAPMPAMNHGHHHGEAHQH

来源 Source

来源生物 organism	Neisseria meningitidis serogroup A
NCBI Class编号 ncbi_taxonomy_id	65699
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	103.863 Å
Unit-cell length b length_b	103.863 Å
Unit-cell length c length_c	31.609 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 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	trigonal

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	44.970 Å
R factor r_factor	0.2228
R_work r_work	0.2175
R_free r_free	0.2708

fit	/app/data/saxs_computation/ya/9yah/9yah.fit
pddf	/app/data/pr_computation/ya/9yah/9yah.pr.out
profile	/app/data/saxs_computation/ya/9yah/9yah.dat

Crystal structure of metallochaperone AccA from Neisseria gonorrhoeae

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

Copper chaperone PCu(A)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

Refinement Refinement

Diffraction experiment Diffraction