SAXSdb — 2gfi

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

phytase

Debaryomyces castellii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	2-acetamido-2-deoxy-beta-D-glucopyranose × 10 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A2TBB4_9SACH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–458； UniProt 4–461 Author chain B； PDBConstruct 1–458； UniProt 4–461

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	2gfi
Deposition date deposition_date	2006-03-22
Structure title title	Crystal structure of the phytase from D. castellii at 2.3 A
Keywords keywords	3-phytase, HYDROLASE; 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.

2gfi__assembly_1__model_1

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

Download this curve (.dat)

2gfi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2gfi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.45 Å
Rg (electron density)	34.12 Å
Total Rg	34.81 Å
Atom count	14524
Residues	1832
Excluded volume	255000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2gfi__assembly_1__model_1`	tetrameric （4）	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	phytase
Molecular weight formula_weight	51063.9 kDa
EC 编号 ec_number	3.1.3.8
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7889

VSKLINNGLLLVGQGAYQDLASPQQASVEQYNIIRFLGGAAPYIQNKGFGISTDIPDQCTLEQVQLFSRHGERYPSTGSGKKYKAVYEKLMSYNGTFKGELAFLNDDYEYFVPDSVYLEKETSPKNSDSIYAGTTDAMKHGIAFRTKYGELFDTNDTLPVFTSNSGRVYQTSQYFARGFMGDDFSNDTVKTNIISEDADMGANSLTPRDGCFNYNENANTAIVDEYTTEYLTKALNRFKASNPGLNITEDDVSNLFGYCAYELNVKGASPMCDIFTNEEFIQYSYSVDLDDYYSNSAGNNMTRVIGSTLLNASLELLNHDKNENKIWLSFTHDTDIEIFHSAIGILIPDEDLPVDYTPFPSPYSHVGITPQGARTIIEKYACGNESYVRYVINDAVIPIKKCSSGPGFSCNLNDYNDYVAERVAGTNYVEQCGNNNASAVTFYWDYETTNYTASLINS

Source Source

Source organism organism	Debaryomyces castellii
NCBI taxonomy ID ncbi_taxonomy_id	27295
Host organism host_organism	Debaryomyces castellii

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	624

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2gfiA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	2gfiB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

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Unit-cell length a length_a	121.655 Å
Unit-cell length b length_b	121.655 Å
Unit-cell length c length_c	332.245 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.290 Å
Low-resolution limit resolution_low	65.230 Å
R factor r_factor	—
R_work r_work	0.1540
R_free r_free	0.2100

Crystal structure of the phytase from D. castellii at 2.3 A

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

phytase

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

2gfi__assembly_1__model_1

2gfi__assembly_1__model_1 | I(q)

2gfi__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the phytase from D. castellii at 2.3 A

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

phytase

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

2gfi__assembly_1__model_1

2gfi__assembly_1__model_1 | I(q)

2gfi__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)