SAXSdb — 8onx

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

Methionine aminopeptidase 2

Thermochaetoides thermophila

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 74–444	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350	Resolution 1.30 Å R-free 0.177

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.

Other PDB	Difference from Current Entry 8ONX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8ONZ Chaetomium thermophilum Methionine Aminopeptidase 2 at the 80S ribosome Deposited 2023-04-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 1–444（444 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
8OO0 Chaetomium thermophilum Methionine Aminopeptidase 2 autoproteolysis product at the 80S ribosome Deposited 2023-04-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 85-meric	Chain D 74–444（371 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	G0SEA9_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–376； UniProt 74–444

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	8onx
Deposition date deposition_date	2023-04-04
最后修订 last_revision	2024-02-14
Structure title title	High resolution structure of Chaetomium thermophilum MAP2
Keywords keywords	;Ribosome Associated Factor, Protease, Tunnel exit, Protein Maturation, Proteostasis, NME, p67, MAP, MetAP, MAP2, MetAP2, ES27L, PTE, 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	21.62 Å
Radius of gyration Rg (electron density) rg_electron	20.59 Å
Forward intensity I(0) i0	29728000.00
Molecular weight molecular_weight	41357.0 kDa
Excluded volume excluded_volume	51511 Å³
Envelope volume envelope_volume	59412 Å³
Hydration-shell volume shell_volume	23674 Å³
Envelope diameter envelope_diameter	68.5 Å
Shell Rg shell_rg	27.75 Å
Envelope Rg envelope_rg	21.03 Å
Shape Rg shape_rg	20.58 Å
Total Rg total_rg	21.49 Å
Total atoms total_atoms	5778
Residues n_residues	371
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	66.4 Å
Rg (real space) rg_real	21.49 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	2.9730e+07
I(0) uncertainty (real space) i0_real_error	3.6660e+05
Rg (reciprocal space) rg_reciprocal	21.52 Å
I(0) (reciprocal space) i0_reciprocal	29730000.0000
Solution quality estimate total_estimate	0.9081
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.4 Å
Skewness Skewness skewness	0.166
Kurtosis Kurtosis kurtosis	-0.498
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8472000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.999

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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	Methionine aminopeptidase 2
Molecular weight formula_weight	41695.8 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	6457

PGSGSPTQQSDPPRVLISHLFPDGKYPAGEEVEYVNENRYRTTSEEKRYLDNMQSEFLNDYRQAAEVHRQVRKWAQGFVKPGKSLIEISEGIEDSVRALVGHPGLEEGDALKAGMGFPVGLSINHCAAHYNPNSGNKIVLQQDDVIKIDIGVHVNGRIVDSAFTMAWNDQFNPLLEAVRAATNAGIREAGIDARVGEIGGVIQEVMESYEVEINGKTYPVKPIRNLNGHNILPYSIHGTKSVPIVKTHDQTKMEEGDVFAIETFGSTGKGYVIESGEVSHYALRGDAPKVDLRLSSAKSLLNVIKRHFGTLPFCRRFLDRLGQEKYLLGLNNLVSNGIVEDYPPLVDEKGSYTAQFEHTILIRPTVKEVISRGDDY

来源 Source

来源生物 organism	Thermochaetoides thermophila
NCBI Class编号 ncbi_taxonomy_id	209285
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	512

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8. Citations (1)

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Unit-cell length a length_a	59.938 Å
Unit-cell length b length_b	73.806 Å
Unit-cell length c length_c	82.049 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	1.300 Å
Low-resolution limit resolution_low	41.020 Å
R factor r_factor	0.1619
R_work r_work	0.1611
R_free r_free	0.1768

fit	/app/data/saxs_computation/on/8onx/8onx.fit
pddf	/app/data/pr_computation/on/8onx/8onx.pr.out
profile	/app/data/saxs_computation/on/8onx/8onx.dat

High resolution structure of Chaetomium thermophilum MAP2

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

Methionine aminopeptidase 2

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