SAXSdb — 1ogo

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

DEXTRANASE

PENICILLIUM MINIOLUTEUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DEXT_PENMI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 1–574； UniProt 35–608

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	1ogo
Deposition date deposition_date	2003-05-08
Structure title title	Dex49A from Penicillium minioluteum complex with isomaltose
Keywords keywords	HYDROLASE, DEXTRAN DEGRADATION, GLYCOSIDASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1ogo__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1ogo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ogo__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	24.20 Å
Rg (electron density)	22.88 Å
Total Rg	23.79 Å
Atom count	4414
Residues	572
Excluded volume	77582 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ogo__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DEXTRANASE
Molecular weight formula_weight	62444.9 kDa
EC 编号 ec_number	3.2.1.11
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	4929

HGTTANTHCGADFCTWWHDSGEINTQTPVQPGNVRQSHKYSVQVSLAGTNNFHDSFVYESIPRNGNGRIYAPTDPPNSNTLDSSVDDGISIEPSIGLNMAWSQFEYSHDVDVKILATDGSSLGSPSDVVIRPVSISYAISQSDDGGIVIRVPADANGRKFSVEFKTDLYTFLSDGNEYVTSGGSVVGVEPTNALVIFASPFLPSGMIPHMTPDNTQTMTPGPINNGDWGAKSILYFPPGVYWMNQDQSGNSGKLGSNHIRLNSNTYWVYLAPGAYVKGAIEYFTKQNFYATGHGILSGENYVYQANAGDNYIAVKSDSTSLRMWWHNNLGGGQTWYCVGPTINAPPFNTMDFNGNSGISSQISDYKQVGAFFFQTDGPEIYPNSVVHDVFWHVNDDAIKIYYSGASVSRATIWKCHNDPIIQMGWTSRDISGVTIDTLNVIHTRYIKSETVVPSAIIGASPFYASGMSPDSRKSISMTVSNVVCEGLCPSLFRITPLQNYKNFVVKNVAFPDGLQTNSIGTGESIIPAASGLTMGLAISAWTIGGQKVTMENFQANSLGQFNIDGSYWGEWQIS

Source Source

Source organism organism	PENICILLIUM MINIOLUTEUM
NCBI taxonomy ID ncbi_taxonomy_id	28574
Host organism host_organism	PICHIA PASTORIS

Entity 2 Entity 2 branched

Description description	alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
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	508

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ogox1
Class class	b — All beta proteins
Fold Fold fold	b.133 — Dextranase, N-terminal domain
Superfamily Superfamily superfamily	b.133.1 — Dextranase, N-terminal domain
Family Family family	b.133.1.1 — Dextranase, N-terminal domain

Domain ID domain_id	d1ogox2
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.1 — Pectin lyase-like
Family Family family	b.80.1.10 — Dextranase, catalytic domain

CATH v4.4 (2 domains)

Domain ID domain_id	1ogoX01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	350 — Dex49a from penicillium minioluteum complex, domain 1
Homologous superfamily homologous superfamily	10 — Dextranase, N-terminal

Domain ID domain_id	1ogoX02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	10 — Single-stranded right-handed beta-helix, Pectin lyase-like

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Unit-cell length a length_a	115.405 Å
Unit-cell length b length_b	103.773 Å
Unit-cell length c length_c	49.740 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	25.730 Å
R factor r_factor	—
R_work r_work	0.1880
R_free r_free	0.2150

Dex49A from Penicillium minioluteum complex with isomaltose

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

DEXTRANASE

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1ogo__assembly_1__model_1

1ogo__assembly_1__model_1 | I(q)

1ogo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Dex49A from Penicillium minioluteum complex with isomaltose

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

DEXTRANASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1ogo__assembly_1__model_1

1ogo__assembly_1__model_1 | I(q)

1ogo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)