SAXSdb — 3d1h

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

Myo-inositol hexaphosphate phosphohydrolase

Selenomonas ruminantium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7WUJ1_SELRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–340； UniProt 28–346 Author chain B； PDBConstruct 22–340； UniProt 28–346

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	3d1h
Deposition date deposition_date	2008-05-05
Structure title title	Structure of the PTP-Like Phytase Expressed by Selenomonas Ruminantium at an Ionic Strength of 500 mM
Keywords keywords	PTP, PROTEIN TYROSINE PHOSPHATASE, PHYTASE, P-LOOP, 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.

3d1h__assembly_1__model_1

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

Download this curve (.dat)

3d1h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d1h__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.98 Å
Rg (electron density)	32.03 Å
Total Rg	32.49 Å
Atom count	5128
Residues	626
Excluded volume	90473 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d1h__assembly_1__model_1`	dimeric （2）	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	Myo-inositol hexaphosphate phosphohydrolase
Molecular weight formula_weight	38987.9 kDa
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	5612

MGSSHHHHHHSSGLVPRGSHMAKAPEQTVTEPVGSYARAERPQDFEGFVWRLDNDGKEALPRNFRTSADALRAPEKKFHLDAAYVPSREGMDALHISGSSAFTPAQLKNVAAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGERDWANLGKSQHEALADERHRLHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQTEQEVAEAAGMRYFRIAATDHVWPTPENIDRFLAFYRTLPQDAWLHFHCEAGVGRTTAFMVMTDMLKNPSVSLKDILYRQHEIGGFYYGEFPIKTKDKDSWKTKYYREKIVMIEQFYRYVQENRADGYQTPWSVWLKSHPAKA

Source Source

Source organism organism	Selenomonas ruminantium
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	484

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3d1ha_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.4 — Myo-inositol hexaphosphate phosphohydrolase (phytase) PhyA

Domain ID domain_id	d3d1hb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.4 — Myo-inositol hexaphosphate phosphohydrolase (phytase) PhyA

CATH v4.4 (4 domains)

Domain ID domain_id	3d1hA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1690 —

Domain ID domain_id	3d1hA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

Domain ID domain_id	3d1hB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1690 —

Domain ID domain_id	3d1hB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

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Unit-cell length a length_a	45.858 Å
Unit-cell length b length_b	137.174 Å
Unit-cell length c length_c	79.839 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.97 °
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	2.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1860
R_work r_work	0.1840
R_free r_free	0.2140

Structure of the PTP-Like Phytase Expressed by Selenomonas Ruminantium at an Ionic Strength of 500 mM

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

Myo-inositol hexaphosphate phosphohydrolase

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

3d1h__assembly_1__model_1

3d1h__assembly_1__model_1 | I(q)

3d1h__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the PTP-Like Phytase Expressed by Selenomonas Ruminantium at an Ionic Strength of 500 mM

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

Myo-inositol hexaphosphate phosphohydrolase

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

3d1h__assembly_1__model_1

3d1h__assembly_1__model_1 | I(q)

3d1h__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)