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2dl1

Solution structure of the MIT domain from human Spartin

Method: SOLUTION NMR Dmax: 51.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Spartin

Homo sapiens

UniProt Q8N0X7

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 8–111 Fragment：MIT domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure ambient NMR sample composition：1.23mM 13C, 15N-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O Resolution not provided

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 2DL1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4U7I Structure of the complex of Spartin MIT and IST1 MIM Deposited 2014-07-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 8–101（94 aa） Fragment：MIT domain (UNP residues 8-101)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；277 K；2.9 M Na-malonate
Resolution 1.79 Å R-free 0.220

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPG20_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–110； UniProt 8–111

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

SAXS profile for 2dl1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2dl1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2dl1
Deposition date deposition_date2006-04-14
Structure title titleSolution structure of the MIT domain from human Spartin
Keywords keywords;Spartin, SPG20, MIT, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, PROTEIN TRANSPORT ;; PROTEIN TRANSPORT
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.46 Å
Radius of gyration Rg (electron density) rg_electron18.82 Å
Forward intensity I(0) i0979195000.00
Molecular weight molecular_weight254650.0 kDa
Excluded volume excluded_volume315960 ų
Envelope volume envelope_volume89971 ų
Hydration-shell volume shell_volume28046 ų
Envelope diameter envelope_diameter105.4 Å
Shell Rg shell_rg33.71 Å
Envelope Rg envelope_rg28.25 Å
Shape Rg shape_rg18.82 Å
Total Rg total_rg19.26 Å
Total atoms total_atoms36180
Residues n_residues2320
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax51.5 Å
Rg (real space) rg_real18.09 Å
Rg uncertainty (real space) rg_real_error0.11 Å
I(0) (real space) i0_real9.3000e+08
I(0) uncertainty (real space) i0_real_error9.3330e+06
Rg (reciprocal space) rg_reciprocal19.79 Å
I(0) (reciprocal space) i0_reciprocal979200000.0000
Solution quality estimate total_estimate0.6724
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary16.7 Å
Skewness Skewness skewness0.368
Kurtosis Kurtosis kurtosis-0.659
Angular range angular_range— – 0.4100 Å−1
Current regularization parameter α current_alpha3.3920
Highest regularization parameter α highest_alpha565900.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.009; Oscil: 0.972; Stabil: 0.983; Sysdev: 0.000; Positv: 1.000; Valcen: 0.880; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2dl1A01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily80 — Phosphotransferase system, lactose/cellobiose-type IIA subunit
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8. Citations (1)

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9. Files and Curves (10)