SAXSdb — 1cpn

▼

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

CIRCULARLY PERMUTED

Paenibacillus macerans

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 82–237	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.80 Å

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 1CPN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AJK CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-84 Deposited 1997-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–237（131 aa）	Not recorded	CA CALCIUM ION × 1 PO4 PHOSPHATE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；SITTING DROP METHOD: A SOLUTION OF 12 MG OF PROTEIN PER ML IN 10 MM HEPES, PH 7.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 50 MM K-PHOSPHATE, PH 7.0 AND 20% (BY WEIGHT) PEG 8000, vapor diffusion - sitting drop	Resolution 1.80 Å R-free 0.219
1AJK CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-84 Deposited 1997-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 107–237（131 aa）	Not recorded	CA CALCIUM ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；SITTING DROP METHOD: A SOLUTION OF 12 MG OF PROTEIN PER ML IN 10 MM HEPES, PH 7.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 50 MM K-PHOSPHATE, PH 7.0 AND 20% (BY WEIGHT) PEG 8000, vapor diffusion - sitting drop	Resolution 1.80 Å R-free 0.219
1AJO CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-127 Deposited 1997-05-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–149（149 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；HANGING DROP METHOD: A SOLUTION OF 18 MG OF PROTEIN PER ML IN 20 MM TRIS/HCL, PH 9.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 0.1 M IMIDAZOLE, PH7.5,2 MM CA-CHLORIDE, 10% (BY WEIGHT) PEG 8000 AND 8% (BY VOL.) ETHYLENE GLYCOL., vapor diffusion - hanging drop	Resolution 2.07 Å R-free 0.235
1AJO CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-127 Deposited 1997-05-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–149（149 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；HANGING DROP METHOD: A SOLUTION OF 18 MG OF PROTEIN PER ML IN 20 MM TRIS/HCL, PH 9.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 0.1 M IMIDAZOLE, PH7.5,2 MM CA-CHLORIDE, 10% (BY WEIGHT) PEG 8000 AND 8% (BY VOL.) ETHYLENE GLYCOL., vapor diffusion - hanging drop	Resolution 2.07 Å R-free 0.235
1AXK ENGINEERED BACILLUS BIFUNCTIONAL ENZYME GLUXYN-1 Deposited 1997-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 82–237（156 aa） Fragment：FUSION OF 1,3-1,4-BETA-GLUCANASE DOMAIN AND 1,4-BETA-XYLANASE DOMAIN Chain B 82–237（156 aa） Fragment：FUSION OF 1,3-1,4-BETA-GLUCANASE DOMAIN AND 1,4-BETA-XYLANASE DOMAIN	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.10 Å R-free 0.224
1CPM NATIVE-LIKE IN VIVO FOLDING OF A CIRCULARLY PERMUTED JELLYROLL PROTEIN SHOWN BY CRYSTAL STRUCTURE ANALYSIS Deposited 1994-03-11	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 82–237（156 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1GLH CATION BINDING TO A BACILLUS (1,3-1,4)-BETA-GLUCANASE. GEOMETRY, AFFINITY AND EFFECT ON PROTEIN STABILITY Deposited 1994-11-25	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–239（214 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.225
1MAC CRYSTAL STRUCTURE AND SITE-DIRECTED MUTAGENESIS OF BACILLUS MACERANS ENDO-1,3-1,4-BETA-GLUCANASE Deposited 1994-12-22	Different construct Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–239（212 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1MAC CRYSTAL STRUCTURE AND SITE-DIRECTED MUTAGENESIS OF BACILLUS MACERANS ENDO-1,3-1,4-BETA-GLUCANASE Deposited 1994-12-22	Different construct Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–239（212 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1U0A Crystal structure of the engineered beta-1,3-1,4-endoglucanase H(A16-M) in complex with beta-glucan tetrasaccharide Deposited 2004-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 40–237（198 aa）	Mutation：E105Q, E109Q	CA CALCIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；293 K；25% (v/v) PEG Monomethyl Ether 550, 0.01 M Zinc Sulfate heptahydrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50	Resolution 1.64 Å R-free 0.197
1U0A Crystal structure of the engineered beta-1,3-1,4-endoglucanase H(A16-M) in complex with beta-glucan tetrasaccharide Deposited 2004-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 40–237（198 aa）	Mutation：E105Q, E109Q	CA CALCIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；293 K；25% (v/v) PEG Monomethyl Ether 550, 0.01 M Zinc Sulfate heptahydrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50	Resolution 1.64 Å R-free 0.197
1U0A Crystal structure of the engineered beta-1,3-1,4-endoglucanase H(A16-M) in complex with beta-glucan tetrasaccharide Deposited 2004-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain C 40–237（198 aa）	Mutation：E105Q, E109Q	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；293 K；25% (v/v) PEG Monomethyl Ether 550, 0.01 M Zinc Sulfate heptahydrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50	Resolution 1.64 Å R-free 0.197
1U0A Crystal structure of the engineered beta-1,3-1,4-endoglucanase H(A16-M) in complex with beta-glucan tetrasaccharide Deposited 2004-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain D 40–237（198 aa）	Mutation：E105Q, E109Q	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；293 K；25% (v/v) PEG Monomethyl Ether 550, 0.01 M Zinc Sulfate heptahydrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50	Resolution 1.64 Å R-free 0.197
1U0A Crystal structure of the engineered beta-1,3-1,4-endoglucanase H(A16-M) in complex with beta-glucan tetrasaccharide Deposited 2004-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 40–237（198 aa） Chain B 40–237（198 aa） Chain C 40–237（198 aa） Chain D 40–237（198 aa）	Mutation：E105Q, E109Q Mutation：E105Q, E109Q Mutation：E105Q, E109Q Mutation：E105Q, E109Q	CA CALCIUM ION × 4 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；293 K；25% (v/v) PEG Monomethyl Ether 550, 0.01 M Zinc Sulfate heptahydrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50	Resolution 1.64 Å R-free 0.197
2AYH CRYSTAL AND MOLECULAR STRUCTURE AT 1.6 ANGSTROMS RESOLUTION OF THE HYBRID BACILLUS ENDO-1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE H(A16-M) Deposited 1995-02-02	Different construct Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–239（214 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å

8 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GUB_PAEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–156； UniProt 82–237

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cpn
Deposition date deposition_date	1994-03-11
Structure title title	NATIVE-LIKE IN VIVO FOLDING OF A CIRCULARLY PERMUTED JELLYROLL PROTEIN SHOWN BY CRYSTAL STRUCTURE ANALYSIS
Keywords keywords	HYDROLASE(GLUCANASE); HYDROLASE(GLUCANASE)
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	16.99 Å
Radius of gyration Rg (electron density) rg_electron	15.71 Å
Forward intensity I(0) i0	9653770.00
Molecular weight molecular_weight	23364.0 kDa
Excluded volume excluded_volume	29177 Å³
Envelope volume envelope_volume	30999 Å³
Hydration-shell volume shell_volume	16241 Å³
Envelope diameter envelope_diameter	50.3 Å
Shell Rg shell_rg	22.04 Å
Envelope Rg envelope_rg	15.85 Å
Shape Rg shape_rg	15.68 Å
Total Rg total_rg	16.79 Å
Total atoms total_atoms	1657
Residues n_residues	208
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

▼

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

Maximum dimension Dmax dmax	51.9 Å
Rg (real space) rg_real	16.84 Å
Rg uncertainty (real space) rg_real_error	0.20 Å
I(0) (real space) i0_real	9.6540e+06
I(0) uncertainty (real space) i0_real_error	9.8870e+04
Rg (reciprocal space) rg_reciprocal	16.86 Å
I(0) (reciprocal space) i0_reciprocal	9654000.0000
Solution quality estimate total_estimate	0.8965
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.5 Å
Skewness Skewness skewness	0.012
Kurtosis Kurtosis kurtosis	-0.502
Angular range angular_range	— – 0.4700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2137000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 1.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CIRCULARLY PERMUTED
Molecular weight formula_weight	23364.7 kDa
EC 编号 ec_number	3.2.1.73
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	1774

FDCAEYRSTNIYGYGLYEVSMKPAKNTGIVSSFFTYTGPAHGTQWDEIDIEFLGKDTTKVQFNYYTNGVGGHEKVISLGFDASKGFHTYAFDWQPGYIKWYVDGVLKHTATANIPSTPGKIMMNLWNGTGVDDWLGSYNGANPLYAEYDWVKYTSNGSVFWEPKSYFNPSTWEKADGYSNGGVFNCTWRANNVNFTNDGKLKLGLTSS

来源 Source

来源生物 organism	Paenibacillus macerans
NCBI Class编号 ncbi_taxonomy_id	44252

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	116

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cpna_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.2 — Glycosyl hydrolases family 16

CATH v4.4 (1 domains)

Domain ID domain_id	1cpnA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

▶

8. Citations (2)

▶

Unit-cell length a length_a	65.470 Å
Unit-cell length b length_b	41.560 Å
Unit-cell length c length_c	39.570 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.46 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1640
R_work r_work	0.1640
R_free r_free	—

fit	/app/data/saxs_computation/cp/1cpn/1cpn.fit
pddf	/app/data/pr_computation/cp/1cpn/1cpn.pr.out
profile	/app/data/saxs_computation/cp/1cpn/1cpn.dat

NATIVE-LIKE IN VIVO FOLDING OF A CIRCULARLY PERMUTED JELLYROLL PROTEIN SHOWN BY CRYSTAL STRUCTURE ANALYSIS

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

CIRCULARLY PERMUTED

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