SAXSdb — 9xg1

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

Protein-asparaginase

Amycolatopsis deserti

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 1–785	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；25% w/v polyethylene glycol 3,350 and Bis-Tris pH6.4	Resolution 2.08 Å R-free 0.244

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	A0ABQ3IKU5_9PSEU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–785； UniProt 1–785

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	9xg1
Deposition date deposition_date	2025-10-29
最后修订 last_revision	2026-04-15
Structure title title	Crystal structure of protein-asparaginase from Amycolatopsis deserti
Keywords keywords	Protein asparaginase, HYDROLASE; HYDROLASE
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	26.55 Å
Radius of gyration Rg (electron density) rg_electron	25.45 Å
Forward intensity I(0) i0	104570000.00
Molecular weight molecular_weight	77901.0 kDa
Excluded volume excluded_volume	96432 Å³
Envelope volume envelope_volume	112740 Å³
Hydration-shell volume shell_volume	35784 Å³
Envelope diameter envelope_diameter	85.3 Å
Shell Rg shell_rg	33.86 Å
Envelope Rg envelope_rg	25.74 Å
Shape Rg shape_rg	25.46 Å
Total Rg total_rg	26.23 Å
Total atoms total_atoms	5483
Residues n_residues	753
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	82.2 Å
Rg (real space) rg_real	26.42 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.0460e+08
I(0) uncertainty (real space) i0_real_error	1.4790e+06
Rg (reciprocal space) rg_reciprocal	26.46 Å
I(0) (reciprocal space) i0_reciprocal	104600000.0000
Solution quality estimate total_estimate	0.9035
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.9 Å
Skewness Skewness skewness	0.216
Kurtosis Kurtosis kurtosis	-0.417
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18150000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.982

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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	Protein-asparaginase
Molecular weight formula_weight	82040.5 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	5743

MRKHWRPAITGAILALGLALLPTPPASAASADGSWSVTPVDGGYRITLTLDKRLPARDASPELAVDGRSLGEAQESRDGRTLTLVTTDPAAAHPSSVRVAWQGVVPGTTPRSATAPTAATDVPAGTPITSAPEAAGHYGVTRADYDFGDTALQLSGLTGVPVEERAAVWVPVGASGKRPVVVFLHGREDACYDPDSGTLDNANWPCVNGLEPMPSYLGYARSAEVLASQGYVVVSVSANAIGAFDQTTASPDRGGLARGQLVMAHLDLLAKADAGTAAGMSPVLKGKLDLGNVGLMGHSRGGDGVVRAALLNAARPTPYGIRGVLPIAPIDRTRPALTDVPMAVLLPYCDGDVSNQEGQHFFEDSRYTSGTDSALKASLLMMGANHNYFNSVWTQVYGDDWDVYVDPGDPACGSSVAGNTRLTVDEQRAAGVAYTAAFFRMTLGRESAFLPMFQSGSGSAVQVGAATVLQATQSPAAQRLDVAPLQAAAGNVAFSGKVLGQYCASIAGASPQSGLPSCSDSTATSRFPSFTPVTHTTNVPATPMLHLTWANGGQMTAALPSGRYDVSRYGALTLRAAPDAGNIAADLQLTVVDGAGRTQSTTVSALSDALSPLPAGNQDLLPKTWLRTVRWPVAAMTLVDTTDIRQIRITTATATGGVLLSDLAFTTPSVGTGAPTKLPQLSVTDTTADEDAGNATVAVRLSKASSLPVTVHLQARTGAGTHITAAAQKVTIPAGQTTATVTIPIQDNSTVDASADTPYQVVLGYPTNAVTGKNTAYVTIHDDEALEHHHHHH

来源 Source

来源生物 organism	Amycolatopsis deserti
NCBI Class编号 ncbi_taxonomy_id	185696
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	260

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8. Citations (1)

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Unit-cell length a length_a	53.654 Å
Unit-cell length b length_b	99.750 Å
Unit-cell length c length_c	114.283 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	48.620 Å
R factor r_factor	0.1830
R_work r_work	0.1799
R_free r_free	0.2442

fit	/app/data/saxs_computation/xg/9xg1/9xg1.fit
pddf	/app/data/pr_computation/xg/9xg1/9xg1.pr.out
profile	/app/data/saxs_computation/xg/9xg1/9xg1.dat

Crystal structure of protein-asparaginase from Amycolatopsis deserti

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

Protein-asparaginase

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 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)