SAXSdb — 2xdv

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

MYC-INDUCED NUCLEAR ANTIGEN

HOMO SAPIENS

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 26–465	Fragment：CATALYTIC DOMAIN, RESIDUES 26-465	OGA N-OXALYLGLYCINE × 6 NI NICKEL (II) ION × 36 MN MANGANESE (II) ION × 6 EDO 1,2-ETHANEDIOL × 12 CD CADMIUM ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions：12% PEG 3350; 0.005M COCL2; 0.005M MGCL2; 0.005M CDCL2; 0.005M NICL2; 0.1M HEPES PH 7.5	Resolution 2.57 Å R-free 0.229
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 26–465	Fragment：CATALYTIC DOMAIN, RESIDUES 26-465	OGA N-OXALYLGLYCINE × 2 NI NICKEL (II) ION × 12 MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 4 CD CADMIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：12% PEG 3350; 0.005M COCL2; 0.005M MGCL2; 0.005M CDCL2; 0.005M NICL2; 0.1M HEPES PH 7.5	Resolution 2.57 Å R-free 0.229

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 2XDV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4BU2 60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with Ni(II) and 2-oxoglutarate (2OG) Deposited 2013-06-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–465（440 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 26-465	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	NI NICKEL (II) ION × 4 AKG 2-OXOGLUTARIC ACID × 2 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M BIS-TRIS PROPANE PH 6.5, 19-22% (W/V) PEG 3350, 0.2M AMMONIUM SULPHATE, 0.005M NICL2, TEMPERATURE 293K. VAPOR DIFFUSION, SITTING DROP	Resolution 2.78 Å R-free 0.233
4BXF 60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) in complex with MN(II), 2-oxoglutarate (2OG) and 60S ribosomal protein L27A (RPL27A G37C) peptide fragment Deposited 2013-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 26–465（440 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 26-465 Chain B 26–465（440 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 26-465	Mutation：YES Mutation：YES	MN MANGANESE (II) ION × 2 AKG 2-OXOGLUTARIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；VAPOR DIFFUSION SITTING DROP. 0.1M BIS-TRIS PROPANE PH 8.5, 0.02M NA-K-PHOSPHATE, 20-22% (W/V) PEG 3350, 0.002 M MNCL2, TEMPERATURE 293K	Resolution 2.05 Å R-free 0.221

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

View Construct and Data Evidence

UniProt name	MINA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–442； UniProt 26–465

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	2xdv
Deposition date deposition_date	2010-05-07
Structure title title	Crystal Structure of the Catalytic Domain of FLJ14393
Keywords keywords	RIBOSOME BIOGENESIS, NUCLEAR PROTEIN; NUCLEAR 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	25.73 Å
Radius of gyration Rg (electron density) rg_electron	24.90 Å
Forward intensity I(0) i0	31706000.00
Molecular weight molecular_weight	43298.0 kDa
Excluded volume excluded_volume	54099 Å³
Envelope volume envelope_volume	71044 Å³
Hydration-shell volume shell_volume	24449 Å³
Envelope diameter envelope_diameter	83.9 Å
Shell Rg shell_rg	31.29 Å
Envelope Rg envelope_rg	25.22 Å
Shape Rg shape_rg	24.84 Å
Total Rg total_rg	25.87 Å
Total atoms total_atoms	3018
Residues n_residues	374
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	81.0 Å
Rg (real space) rg_real	25.74 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	3.1710e+07
I(0) uncertainty (real space) i0_real_error	4.4010e+05
Rg (reciprocal space) rg_reciprocal	25.74 Å
I(0) (reciprocal space) i0_reciprocal	31710000.0000
Solution quality estimate total_estimate	0.9068
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.302
Kurtosis Kurtosis kurtosis	-0.599
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3851000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	MYC-INDUCED NUCLEAR ANTIGEN
Molecular weight formula_weight	50462.3 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	3222

SMAAGGPSALNFDSPSSLFESLISPIKTETFFKEFWEQKPLLIQRDDPALATYYGSLFKLTDLKSLCSRGMYYGRDVNVCRCVNGKKKVLNKDGKAHFLQLRKDFDQKRATIQFHQPQRFKDELWRIQEKLECYFGSLVGSNVYITPAGSQGLPPHYDDVEVFILQLEGEKHWRLYHPTVPLAREYSVEAEERIGRPVHEFMLKPGDLLYFPRGTIHQADTPAGLAHSTHVTISTYQNNSWGDFLLDTISGLVFDTAKEDVELRTGIPRQLLLQVESTTVATRRLSGFLRTLADRLEGTKELLSSDMKKDFIMHRLPPYSAGDGAELSTPGGKLPRLDSVVRLQFKDHIVLTVLPDQDQSDETQEKMVYIYHSLKNSRETHMMGNEEETEFHGLRFPLSHLDALKQIWNSPAISVKDLKLTTDEEKESLVLSLWTECLIQVV

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	N-OXALYLGLYCINE
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	148

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	2xdvA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	2xdvA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1500 — JmjC domain-containing ribosomal oxygenase (ROX), dimer domain

Domain ID domain_id	2xdvA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Unit-cell length a length_a	185.180 Å
Unit-cell length b length_b	185.180 Å
Unit-cell length c length_c	185.180 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	24

Space group space_group	P 43 3 2
Space-group number int_tables_number	212
Crystal system crystal_system	—

Resolution resolution	2.570 Å
Low-resolution limit resolution_low	29.280 Å
R factor r_factor	0.1981
R_work r_work	0.1965
R_free r_free	0.2285

fit	/app/data/saxs_computation/xd/2xdv/2xdv.fit
pddf	/app/data/pr_computation/xd/2xdv/2xdv.pr.out
profile	/app/data/saxs_computation/xd/2xdv/2xdv.dat

Crystal Structure of the Catalytic Domain of FLJ14393