SAXSdb — 2bdx

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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–323	Not recorded	DIHYDROMICROCYSTIN-LA × 1 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

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 2BDX	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 oligomeric state 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 oligomeric state 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
1JK7 CRYSTAL STRUCTURE OF THE TUMOR-PROMOTER OKADAIC ACID BOUND TO PROTEIN PHOSPHATASE-1 Deposited 2001-07-11	Different oligomeric state 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 oligomeric state 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 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
4UT2 X-ray structure of the human PP1 gamma catalytic subunit treated with ascorbate Deposited 2014-07-17	Different mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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	2bdx
Deposition date deposition_date	2005-10-21
Structure title title	X-ray Crystal Structure of dihydromicrocystin-LA bound to Protein Phosphatase-1
Keywords keywords	Protein phosphatase, natural product inhibitors, microcystins, nodularins, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
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	19.21 Å
Radius of gyration Rg (electron density) rg_electron	18.05 Å
Forward intensity I(0) i0	19375900.00
Molecular weight molecular_weight	34252.0 kDa
Excluded volume excluded_volume	43142 Å³
Envelope volume envelope_volume	47981 Å³
Hydration-shell volume shell_volume	21327 Å³
Envelope diameter envelope_diameter	60.0 Å
Shell Rg shell_rg	25.22 Å
Envelope Rg envelope_rg	18.44 Å
Shape Rg shape_rg	18.05 Å
Total Rg total_rg	19.04 Å
Total atoms total_atoms	2405
Residues n_residues	295
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	59.0 Å
Rg (real space) rg_real	19.07 Å
Rg uncertainty (real space) rg_real_error	0.18 Å
I(0) (real space) i0_real	1.9380e+07
I(0) uncertainty (real space) i0_real_error	2.1540e+05
Rg (reciprocal space) rg_reciprocal	19.09 Å
I(0) (reciprocal space) i0_reciprocal	19380000.0000
Solution quality estimate total_estimate	0.8972
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.6 Å
Skewness Skewness skewness	0.153
Kurtosis Kurtosis kurtosis	-0.373
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6598000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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	2440

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 polymer

Description description	DIHYDROMICROCYSTIN-LA
Molecular weight formula_weight	930.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ALDAXEA

Entity 3 Entity 3 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 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	35

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2bdxa_
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	2bdxA00
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	99.978 Å
Unit-cell length b length_b	99.978 Å
Unit-cell length c length_c	62.949 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	2.300 Å
Low-resolution limit resolution_low	35.360 Å
R factor r_factor	0.2140
R_work r_work	0.2120
R_free r_free	0.2500

fit	/app/data/saxs_computation/bd/2bdx/2bdx.fit
pddf	/app/data/pr_computation/bd/2bdx/2bdx.pr.out
profile	/app/data/saxs_computation/bd/2bdx/2bdx.dat

X-ray Crystal Structure of dihydromicrocystin-LA bound to Protein Phosphatase-1

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

Serine/threonine protein phosphatase PP1-gamma catalytic subunit

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)