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6z90

Crystal structure of MINDY1 mutant-P138A

Method: X-RAY DIFFRACTION Dmax: 70.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin carboxyl-terminal hydrolase MINDY-1

Homo sapiens

UniProt Q8N5J2

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 110–384 Mutation：P138A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.7 M sodium citrate tribasic dihydrate, 0.1 M BIS-TRIS propane pH 7.0 Resolution 3.59 Å R-free 0.258

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 6Z90 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5JKN Crystal structure of deubiquitinase MINDY-1 Deposited 2016-04-26 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–384（275 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 PO4 PHOSPHATE ION × 1 HG MERCURY (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；100mM Hepes-Na pH 7.5, 200mM NaCl and 25% PEG4000
Resolution 3.00 Å R-free 0.242
5JQS Crystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin Deposited 2016-05-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 110–384（275 aa）
Not recorded AYE prop-2-en-1-amine × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 1 DIO 1,4-DIETHYLENE DIOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；100mM MES, 10% Dioxane and 1.6 M ammonium sulphate
Resolution 2.65 Å R-free 0.231
5MN9 Crystal structure of MINDY-1 tMIU in complex with K48-diUb Deposited 2016-12-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 388–426（39 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293.15 K；100 mM sodium acetate pH 5.4 and 18.5 % PEG3350
Resolution 2.05 Å R-free 0.223
6TUV Crystal structure of Mindy1 in complex with Lys48 linked di-ubiquitin Deposited 2020-01-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 110–384（275 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；100 mM Tris-HCl, 200mM LiSO4.H2O, 30% PEG400
Resolution 2.16 Å R-free 0.249
6TXB Crystal structure of Mindy1 mutant (P138A) in complex with Lys48 linked di-ubiquitin Deposited 2020-01-14 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 110–384（275 aa）
Mutation：C137A, P138A NA SODIUM ION × 4 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.2 M Sodium malonate, 20% PEG 3350
Resolution 2.18 Å R-free 0.246
6Y6R Crystal structure of MINDY1 T335D mutant Deposited 2020-02-27 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–384（275 aa）
Mutation：T335D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.1 M HEPES sodium pH 7.5, 0.8 M Potassium sodium tartrate tetrahydrate
Resolution 3.32 Å R-free 0.243

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MINY1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 15–289； UniProt 110–384

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 6z90

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6z90
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6z90
Deposition date deposition_date2020-06-03
Structure title titleCrystal structure of MINDY1 mutant-P138A
Keywords keywordsHYDROLASE, CYSTEINE PROTEASE, ISOPEPTIDASE AND UBIQUITIN BINDING; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.87 Å
Radius of gyration Rg (electron density) rg_electron19.82 Å
Forward intensity I(0) i013719000.00
Molecular weight molecular_weight27607.0 kDa
Excluded volume excluded_volume34379 ų
Envelope volume envelope_volume42015 ų
Hydration-shell volume shell_volume18461 ų
Envelope diameter envelope_diameter73.9 Å
Shell Rg shell_rg25.57 Å
Envelope Rg envelope_rg20.07 Å
Shape Rg shape_rg19.81 Å
Total Rg total_rg20.68 Å
Total atoms total_atoms1946
Residues n_residues256
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 dmax70.6 Å
Rg (real space) rg_real20.87 Å
Rg uncertainty (real space) rg_real_error0.55 Å
I(0) (real space) i0_real1.3720e+07
I(0) uncertainty (real space) i0_real_error1.9030e+05
Rg (reciprocal space) rg_reciprocal20.87 Å
I(0) (reciprocal space) i0_reciprocal13720000.0000
Solution quality estimate total_estimate0.7965
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.5 Å
Skewness Skewness skewness0.380
Kurtosis Kurtosis kurtosis-0.159
Angular range angular_range— – 0.3800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3016000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.792; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; 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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8. Citations (1)

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9. Files and Curves (10)