SAXSdb — 7qfa

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

Protein phosphatase 1 regulatory subunit 3C

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	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 132–264	Fragment：CBM21 domain (residues 132-264) Mutation：First residue S derives from the expression tag	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；25% PEG 1500	Resolution 2.00 Å R-free 0.212
2	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 132–264	Fragment：CBM21 domain (residues 132-264) Mutation：First residue S derives from the expression tag	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；25% PEG 1500	Resolution 2.00 Å R-free 0.212
3	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 132–264	Fragment：CBM21 domain (residues 132-264) Mutation：First residue S derives from the expression tag	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；25% PEG 1500	Resolution 2.00 Å R-free 0.212

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 7QFA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7QF7 Orthorhombic crystal structure of PTG CBM21 in complex with beta-cyclodextrin Deposited 2021-12-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 132–264（133 aa） Fragment：CBM21 domain (residues 132-264)	Mutation：First residue S derives from the expression tag	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；3 M NaCl	Resolution 1.47 Å R-free 0.195
7QFB Crystal structure of Protein Phosphatase 1 in complex with PP1-binding peptide from PTG Deposited 2021-12-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 81–107（27 aa） Fragment：peptide 81-107	Not recorded	GOL GLYCEROL × 8 MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.6 M Lithium sulfate, 1.4 M sodium malonate	Resolution 2.05 Å R-free 0.191
7QM2 Crystal structure of the PP1/PTG/beta-cyclodextrin ternary complex Deposited 2021-12-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 70–264（195 aa） Fragment：residues 70-264)	Mutation：First residues GPLGS derive from the expression tag	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium acetate, 1 M sodium malonate	Resolution 2.69 Å R-free 0.213
7QM2 Crystal structure of the PP1/PTG/beta-cyclodextrin ternary complex Deposited 2021-12-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 70–264（195 aa） Fragment：residues 70-264)	Mutation：First residues GPLGS derive from the expression tag	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium acetate, 1 M sodium malonate	Resolution 2.69 Å R-free 0.213

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

View Construct and Data Evidence

UniProt name	PPR3C_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–134； UniProt 132–264 Author chain B； PDBConstruct 2–134； UniProt 132–264 Author chain C； PDBConstruct 2–134； UniProt 132–264

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	7qfa
Deposition date deposition_date	2021-12-05
Structure title title	Monoclinic crystal structure of PTG CBM21 in complex with beta-cyclodextrin
Keywords keywords	carbohydrate binding, immunoglobulin-like fold, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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	25.02 Å
Radius of gyration Rg (electron density) rg_electron	24.03 Å
Forward intensity I(0) i0	38917200.00
Molecular weight molecular_weight	47877.0 kDa
Excluded volume excluded_volume	59745 Å³
Envelope volume envelope_volume	76155 Å³
Hydration-shell volume shell_volume	26528 Å³
Envelope diameter envelope_diameter	76.0 Å
Shell Rg shell_rg	31.02 Å
Envelope Rg envelope_rg	23.60 Å
Shape Rg shape_rg	24.02 Å
Total Rg total_rg	24.90 Å
Total atoms total_atoms	3368
Residues n_residues	379
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	75.7 Å
Rg (real space) rg_real	24.89 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	3.8920e+07
I(0) uncertainty (real space) i0_real_error	5.4480e+05
Rg (reciprocal space) rg_reciprocal	24.93 Å
I(0) (reciprocal space) i0_reciprocal	38920000.0000
Solution quality estimate total_estimate	0.9134
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.8 Å
Skewness Skewness skewness	0.081
Kurtosis Kurtosis kurtosis	-0.592
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11310000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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	Protein phosphatase 1 regulatory subunit 3C
Molecular weight formula_weight	15647.5 kDa
Mutation mutation	First residue S derives from the expression tag
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3609

SKNLILDFPQPSTDYLSFRSHFQKNFVCLENCSLQERTVTGTVKVKNVSFEKKVQIRITFDSWKNYTDVDCVYMKNVYGGTDSDTFSFAIDLPPVIPTEQKIEFCISYHANGQVFWDNNDGQNYRIVHVQWKPD

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 branched

Description description	Cycloheptakis-(1-4)-(alpha-D-glucopyranose)
Molecular weight formula_weight	1153.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	236

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	7qfaA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2440 — Carbohydrate binding type-21 domain

Domain ID domain_id	7qfaB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2440 — Carbohydrate binding type-21 domain

Domain ID domain_id	7qfaC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2440 — Carbohydrate binding type-21 domain

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8. Citations (1)

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Unit-cell length a length_a	66.830 Å
Unit-cell length b length_b	42.866 Å
Unit-cell length c length_c	168.994 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	41.506 Å
R factor r_factor	0.1750
R_work r_work	0.1731
R_free r_free	0.2117

fit	/app/data/saxs_computation/qf/7qfa/7qfa.fit
pddf	/app/data/pr_computation/qf/7qfa/7qfa.pr.out
profile	/app/data/saxs_computation/qf/7qfa/7qfa.dat

Monoclinic crystal structure of PTG CBM21 in complex with beta-cyclodextrin

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

Protein phosphatase 1 regulatory subunit 3C

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