SAXSdb — 1jk7

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1. Protein Identity and Related Structures Protein Identity & Related Structures

SERINE/THREONINE PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT

Homo sapiens

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 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

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 1JK7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1IT6 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CALYCULIN A AND THE CATALYTIC SUBUNIT OF PROTEIN PHOSPHATASE 1 Deposited 2002-01-09	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 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
1IT6 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CALYCULIN A AND THE CATALYTIC SUBUNIT OF PROTEIN PHOSPHATASE 1 Deposited 2002-01-09	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）	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
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 14 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

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1jk7
Deposition date deposition_date	2001-07-11
Structure title title	CRYSTAL STRUCTURE OF THE TUMOR-PROMOTER OKADAIC ACID BOUND TO PROTEIN PHOSPHATASE-1
Keywords keywords	HYDROLASE-INHIBITOR COMPLEX, HYDROLASE-TOXIN COMPLEX; HYDROLASE/TOXIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.31 Å
Radius of gyration Rg (electron density) rg_electron	18.12 Å
Forward intensity I(0) i0	20164100.00
Molecular weight molecular_weight	34971.0 kDa
Excluded volume excluded_volume	44035 Å³
Envelope volume envelope_volume	48516 Å³
Hydration-shell volume shell_volume	21462 Å³
Envelope diameter envelope_diameter	60.5 Å
Shell Rg shell_rg	25.32 Å
Envelope Rg envelope_rg	18.53 Å
Shape Rg shape_rg	18.11 Å
Total Rg total_rg	19.14 Å
Total atoms total_atoms	2447
Residues n_residues	294
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	61.7 Å
Rg (real space) rg_real	19.17 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	2.0160e+07
I(0) uncertainty (real space) i0_real_error	2.2430e+05
Rg (reciprocal space) rg_reciprocal	19.19 Å
I(0) (reciprocal space) i0_reciprocal	20160000.0000
Solution quality estimate total_estimate	0.8853
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.158
Kurtosis Kurtosis kurtosis	-0.374
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6774000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.990

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	SERINE/THREONINE PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
Molecular weight formula_weight	37030.8 kDa
EC 编号 ec_number	3.1.3.16
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2625

MADLDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAEKKKPNATRPVTPPRGMITKQAKK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	OKADAIC ACID
Molecular weight formula_weight	805.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	178

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1jk7a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
Family Family family	d.159.1.3 — Protein serine/threonine phosphatase

CATH v4.4 (1 domains)

Domain ID domain_id	1jk7A00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

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8. Citations (1)

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Unit-cell length a length_a	99.180 Å
Unit-cell length b length_b	99.180 Å
Unit-cell length c length_c	62.170 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	29.660 Å
R factor r_factor	0.1990
R_work r_work	0.1990
R_free r_free	0.2250

fit	/app/data/saxs_computation/jk/1jk7/1jk7.fit
pddf	/app/data/pr_computation/jk/1jk7/1jk7.pr.out
profile	/app/data/saxs_computation/jk/1jk7/1jk7.dat

CRYSTAL STRUCTURE OF THE TUMOR-PROMOTER OKADAIC ACID BOUND TO PROTEIN PHOSPHATASE-1