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1it6

CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CALYCULIN A AND THE CATALYTIC SUBUNIT OF PROTEIN PHOSPHATASE 1

Method: X-RAY DIFFRACTION Dmax: 115.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SERINE/THREONINE PROTEIN PHOSPHATASE 1 GAMMA (PP1-GAMMA) CATALYTIC SUBUNIT

Homo sapiens

UniProt P36873

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 1–323 Not recorded MN MANGANESE (II) ION × 2 CYU CALYCULIN A × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；PEG3350, POTASSIUM SULFATE, MANGANESE(II) CHLORIDE, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.00 Å R-free 0.218
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–323 Not recorded MN MANGANESE (II) ION × 2 CYU CALYCULIN A × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；PEG3350, POTASSIUM SULFATE, MANGANESE(II) CHLORIDE, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.00 Å R-free 0.218

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 1IT6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1JK7 CRYSTAL STRUCTURE OF THE TUMOR-PROMOTER OKADAIC ACID BOUND TO PROTEIN PHOSPHATASE-1 Deposited 2001-07-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–323（323 aa）
Not recorded MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 1 OKA OKADAIC ACID × 1 BME BETA-MERCAPTOETHANOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；LITHIUM SULPHATE, PEG 400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.225
1U32 Crystal structure of a Protein Phosphatase-1: Calcineurin Hybrid Bound to Okadaic Acid Deposited 2004-07-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 6–298（293 aa） Fragment：residues 6-298
Not recorded MN MANGANESE (II) ION × 2 OKA OKADAIC ACID × 1 BME BETA-MERCAPTOETHANOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；lithium sulfate, tris, PEG 400, mercaptoethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.254
2BCD X-ray crystal structure of Protein Phosphatase-1 with the marine toxin motuporin bound Deposited 2005-10-19 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 1–323（323 aa）
Not recorded BME BETA-MERCAPTOETHANOL × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；273 K；2.3 M lithium sulfate, Tris-HCl (100 mM, pH 8.0), polyethylene glycol 400 (2%), beta-mercaptoethanol (10 mM), VAPOR DIFFUSION, HANGING DROP, temperature 273K
Resolution 2.10 Å R-free 0.264
2BDX X-ray Crystal Structure of dihydromicrocystin-LA bound to Protein Phosphatase-1 Deposited 2005-10-21 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 1–323（323 aa）
Not recorded MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；273 K；2.3 M lithium sulfate, Tris-HCl (100 mM, pH 8.0), polyethylene glycol 400 (2%) and beta-mercaptoethanol (10 mM), VAPOR DIFFUSION, HANGING DROP, temperature 273K
Resolution 2.30 Å R-free 0.250
4UT2 X-ray structure of the human PP1 gamma catalytic subunit treated with ascorbate Deposited 2014-07-17 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 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；19.3 % PEG 3350, 200 MM NACL, 100 MM TRIS PH 9.0 SOAKING IN RESERVOIR ENRICHED BY 25MM ASCORBATE FOR 30 MINUTES CRYOPROTECTION 20% GLYCEROL
Resolution 1.96 Å R-free 0.201
4UT2 X-ray structure of the human PP1 gamma catalytic subunit treated with ascorbate Deposited 2014-07-17 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；19.3 % PEG 3350, 200 MM NACL, 100 MM TRIS PH 9.0 SOAKING IN RESERVOIR ENRICHED BY 25MM ASCORBATE FOR 30 MINUTES CRYOPROTECTION 20% GLYCEROL
Resolution 1.96 Å R-free 0.201
4UT3 X-ray structure of the human PP1 gamma catalytic subunit treated with hydrogen peroxide Deposited 2014-07-17 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 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；7-12% PEG3350, 0.1 M BICINE, PH 9.0 SOAKING IN RESERVOIR ENRICHED WITH 50MM H2O2 FOR 10 MINS CRYOPROTECTION IN RESEVOIR ENRICHED WITH 25% MPD
Resolution 2.19 Å R-free 0.211
4UT3 X-ray structure of the human PP1 gamma catalytic subunit treated with hydrogen peroxide Deposited 2014-07-17 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；7-12% PEG3350, 0.1 M BICINE, PH 9.0 SOAKING IN RESERVOIR ENRICHED WITH 50MM H2O2 FOR 10 MINS CRYOPROTECTION IN RESEVOIR ENRICHED WITH 25% MPD
Resolution 2.19 Å R-free 0.211
5INB RepoMan-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex Deposited 2016-03-07 Different construct 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 7–308（302 aa） Fragment：UNP residues 7-308
Not recorded MLI MALONATE ION × 1 GOL GLYCEROL × 6 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.3；277 K；1 M Sodium Malonate
Resolution 1.30 Å R-free 0.153
5J28 Ki67-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex Deposited 2016-03-29 Different construct 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 7–308（302 aa） Fragment：UNP residues 7-308
Not recorded MLI MALONATE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；1.9 M Sodium Malonate pH 4.0
Resolution 2.00 Å R-free 0.197
5J28 Ki67-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex Deposited 2016-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 7–308（302 aa） Fragment：UNP residues 7-308
Not recorded MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；1.9 M Sodium Malonate pH 4.0
Resolution 2.00 Å R-free 0.197
7SD0 Cryo-EM structure of the SHOC2:PP1C:MRAS complex Deposited 2021-09-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–323（323 aa）
Not recorded GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Used the "perpetually hydrated" method of applying graphene oxide. (Cheung et al., 2018)
Resolution 2.95 Å
8B5R p97-p37-SPI substrate complex Deposited 2022-09-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain P 1–323（323 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.10 Å

10 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PP1G_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–323； UniProt 1–323 Author chain B； PDBConstruct 1–323； UniProt 1–323

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 1it6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1it6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1it6
Deposition date deposition_date2002-01-09
Structure title titleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CALYCULIN A AND THE CATALYTIC SUBUNIT OF PROTEIN PHOSPHATASE 1
Keywords keywordsHYDROLASE-INHIBITOR COMPLEX, HYDROLASE; 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_guinier35.49 Å
Radius of gyration Rg (electron density) rg_electron35.39 Å
Forward intensity I(0) i069713600.00
Molecular weight molecular_weight69021.0 kDa
Excluded volume excluded_volume86931 ų
Envelope volume envelope_volume109640 ų
Hydration-shell volume shell_volume25722 ų
Envelope diameter envelope_diameter116.4 Å
Shell Rg shell_rg42.04 Å
Envelope Rg envelope_rg34.63 Å
Shape Rg shape_rg35.38 Å
Total Rg total_rg35.89 Å
Total atoms total_atoms4840
Residues n_residues586
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 dmax115.3 Å
Rg (real space) rg_real35.78 Å
Rg uncertainty (real space) rg_real_error0.92 Å
I(0) (real space) i0_real6.9710e+07
I(0) uncertainty (real space) i0_real_error1.0910e+06
Rg (reciprocal space) rg_reciprocal35.61 Å
I(0) (reciprocal space) i0_reciprocal69700000.0000
Solution quality estimate total_estimate0.6806
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.6 Å
Skewness Skewness skewness0.300
Kurtosis Kurtosis kurtosis-1.053
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha66750000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.202; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.382; Smooth: 0.856
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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1it6a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.3 — Protein serine/threonine phosphatase
Domain ID domain_idd1it6b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.3 — Protein serine/threonine phosphatase

CATH v4.4 (2 domains)

Domain ID domain_id1it6A00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
Domain ID domain_id1it6B00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
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8. Citations (1)

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9. Files and Curves (10)