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1gjz

Solution structure of a dimeric N-terminal fragment of human ubiquitin

Method: SOLUTION NMR Dmax: 42.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

UBIQUITIN

HOMO SAPIENS

UniProt P02248

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–51 Chain B； UniProt 1–51 Fragment：RESIDUES 1-51 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 800MM SODIUM SULPHATE；Pressure 1 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 1GJZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CMX STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL HYDROLASES Deposited 1999-05-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–75（75 aa） Fragment：ALL
Chain D 1–75（75 aa） Fragment：ALL
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；16% PEG 6000 0.1 M SODIUM ACETATE PH 4.4, pH 4.5
Resolution 2.25 Å R-free 0.285
1UD7 SOLUTION STRUCTURE OF THE DESIGNED HYDROPHOBIC CORE MUTANT OF UBIQUITIN, 1D7 Deposited 1999-04-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 41–116（76 aa）
Mutation：I3V,V5L,I13V,L15I,I23V,V26F,I67L No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；303 K；Pressure 1
Resolution not provided
1UZX A complex of the Vps23 UEV with ubiquitin Deposited 2004-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；22% PEG 8000, 0.1M MES PH 6.5, 0.2M (NH4)2SO4
Resolution 1.85 Å R-free 0.274

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBIQ_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–53； UniProt 1–51 Author chain B； PDBConstruct 3–53； UniProt 1–51

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 1gjz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1gjz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1gjz
Deposition date deposition_date2001-08-06
Structure title titleSolution structure of a dimeric N-terminal fragment of human ubiquitin
Keywords keywordsUBIQUITIN, DIMER, PROTEIN DISSECTION; UBIQUITIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.79 Å
Radius of gyration Rg (electron density) rg_electron13.27 Å
Forward intensity I(0) i0461733000.00
Molecular weight molecular_weight188280.0 kDa
Excluded volume excluded_volume239030 ų
Envelope volume envelope_volume25100 ų
Hydration-shell volume shell_volume14159 ų
Envelope diameter envelope_diameter48.2 Å
Shell Rg shell_rg20.85 Å
Envelope Rg envelope_rg15.14 Å
Shape Rg shape_rg13.26 Å
Total Rg total_rg13.51 Å
Total atoms total_atoms27072
Residues n_residues1696
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 dmax42.2 Å
Rg (real space) rg_real13.68 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real4.6170e+08
I(0) uncertainty (real space) i0_real_error4.9710e+06
Rg (reciprocal space) rg_reciprocal13.69 Å
I(0) (reciprocal space) i0_reciprocal461700000.0000
Solution quality estimate total_estimate0.8929
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.0 Å
Skewness Skewness skewness-0.003
Kurtosis Kurtosis kurtosis-0.486
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha191800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.877; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.997
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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1gjza_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd1gjzb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related

CATH v4.4 (2 domains)

Domain ID domain_id1gjzA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id1gjzB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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8. Citations (1)

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9. Files and Curves (10)