SAXSdb — 3k4p

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

3-phytase A

Aspergillus niger

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHYA_ASPNG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–444； UniProt 24–467 Author chain B； PDBConstruct 1–444； UniProt 24–467

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	3k4p
Deposition date deposition_date	2009-10-06
Structure title title	Aspergillus niger Phytase
Keywords keywords	;Phytase, PhyA, 3-Phosphotase, myo-inositol hexakis phosphate phosphohydrolase, 37288-11-2, Disulfide bond, Glycoprotein, Hydrolase, Secreted ;; 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.

3k4p__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3k4p__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3k4p__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	23.24 Å
Rg (electron density)	22.23 Å
Total Rg	23.17 Å
Atom count	3431
Residues	438
Excluded volume	60406 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3k4p__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3k4p__assembly_2__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	3-phytase A
Molecular weight formula_weight	48889.0 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	7195

ASRNQSSCDTVDQGYQCFSETSHLWGQYAPFFSLANESVISPEVPAGCRVTFAQVLSRHGARYPTDSKGKKYSALIEEIQQNATTFDGKYAFLKTYNYSLGADDLTPFGEQELVNSGIKFYQRYESLTRNIVPFIRSSGSSRVIASGKKFIEGFQSTKLKDPRAQPGQSSPKIDVVISEASSSNNTLDPGTCTVFEDSELADTVEANFTATFVPSIRQRLENDLSGVTLTDTEVTYLMDMCSFDTISTSTVDTKLSPFCDLFTHDEWINYDYLQSLKKYYGHGAGNPLGPTQGVGYANELIARLTHSPVHDDTSSNHTLDSSPATFPLNSTLYADFSHDNGIISILFALGLYNGTKPLSTTTVENITQTDGFSSAWTVPFASRLYVEMMQCQAEQEPLVRVLVNDRVVPLHGCPVDALGRCTRDSFVRGLSFARSGGDWAECFA

Source Source

Source organism organism	Aspergillus niger
NCBI taxonomy ID ncbi_taxonomy_id	5061
Host organism host_organism	Aspergillus niger

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	man
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	316

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3k4pa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.2 — Histidine acid phosphatase

Domain ID domain_id	d3k4pb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.2 — Histidine acid phosphatase

CATH v4.4 (2 domains)

Domain ID domain_id	3k4pA01
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	3k4pB01
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	71.066 Å
Unit-cell length b length_b	87.457 Å
Unit-cell length c length_c	82.185 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	66.360 Å
R factor r_factor	0.2182
R_work r_work	0.2153
R_free r_free	0.2755

Aspergillus niger Phytase

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

3-phytase A

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

3k4p__assembly_2__model_1

3k4p__assembly_2__model_1 | I(q)

3k4p__assembly_2__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Aspergillus niger Phytase

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

3-phytase A

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

3k4p__assembly_2__model_1

3k4p__assembly_2__model_1 | I(q)

3k4p__assembly_2__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)