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4mew

Structure of the core fragment of human PR70

Method: X-RAY DIFFRACTION Dmax: 86.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

;Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta ;

Homo sapiens

UniProt Q9Y5P8

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 130–483 Fragment：Residues 130-483 Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；277 K；0.1 M Tris-HCl, 16% PEG 2000 monomethyl ether, 0.15 M trimethylamine N-oxide, pH 7.5, VAPOR DIFFUSION, temperature 277K Resolution 1.99 Å R-free 0.193

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 4MEW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4I5L Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6 dephosphorylation Deposited 2012-11-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 122–490（369 aa） Fragment：UNP Q9Y5P8 residues 122-490 and UNP Q99741 residues 70-90
Not recorded PEG DI(HYDROXYETHYL)ETHER × 8 CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2 MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；292 K；0.1M Na Malonate, 12% PEG 3350 + 6.2mg/mL protein in buffer Tris, 150mM NaCl , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.43 Å R-free 0.228
4I5L Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6 dephosphorylation Deposited 2012-11-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 122–490（369 aa） Fragment：UNP Q9Y5P8 residues 122-490 and UNP Q99741 residues 70-90
Not recorded PEG DI(HYDROXYETHYL)ETHER × 3 CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2 MLI MALONATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；292 K；0.1M Na Malonate, 12% PEG 3350 + 6.2mg/mL protein in buffer Tris, 150mM NaCl , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.43 Å R-free 0.228
4I5N Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6 dephosphorylation Deposited 2012-11-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 122–490（369 aa） Fragment：UNP Q9Y5P8 residues 122-490 and UNP Q99741 residues 70-90
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；296 K；0.03M Succinic acid with 7% PEG 3350. Protein (6.2mg/mL) in 10mM tris pH 8.0, 150mM NaCl, 5mM DTT, 1mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.80 Å R-free 0.250
4I5N Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6 dephosphorylation Deposited 2012-11-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 122–490（369 aa） Fragment：UNP Q9Y5P8 residues 122-490 and UNP Q99741 residues 70-90
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；296 K；0.03M Succinic acid with 7% PEG 3350. Protein (6.2mg/mL) in 10mM tris pH 8.0, 150mM NaCl, 5mM DTT, 1mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.80 Å R-free 0.250

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name P2R3B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–356； UniProt 130–483

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 4mew

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4mew
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4mew
Deposition date deposition_date2013-08-27
Structure title titleStructure of the core fragment of human PR70
Keywords keywordsEF-hands, Protein Phosphatase, Calcium Binding, METAL BINDING PROTEIN, hydrolase, cell cycle; hydrolase, cell cycle
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_guinier25.20 Å
Radius of gyration Rg (electron density) rg_electron24.25 Å
Forward intensity I(0) i029197500.00
Molecular weight molecular_weight41078.0 kDa
Excluded volume excluded_volume50995 ų
Envelope volume envelope_volume62224 ų
Hydration-shell volume shell_volume22490 ų
Envelope diameter envelope_diameter88.6 Å
Shell Rg shell_rg30.21 Å
Envelope Rg envelope_rg24.61 Å
Shape Rg shape_rg24.20 Å
Total Rg total_rg25.15 Å
Total atoms total_atoms2858
Residues n_residues339
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 dmax86.3 Å
Rg (real space) rg_real25.34 Å
Rg uncertainty (real space) rg_real_error0.74 Å
I(0) (real space) i0_real2.9200e+07
I(0) uncertainty (real space) i0_real_error4.6100e+05
Rg (reciprocal space) rg_reciprocal25.30 Å
I(0) (reciprocal space) i0_reciprocal29200000.0000
Solution quality estimate total_estimate0.8537
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.6 Å
Skewness Skewness skewness0.508
Kurtosis Kurtosis kurtosis-0.252
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5163000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.786; Smooth: 0.964
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id4mewA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily230 —
Domain ID domain_id4mewA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily220 —
Domain ID domain_id4mewA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
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8. Citations (1)

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9. Files and Curves (10)