SAXSdb — 9gvd

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

Multifunctional alkaline phosphatase superfamily protein pRL90232

Rhizobium johnstonii 3841

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	MANGANESE (II) ION × 4 VANADATE ION × 4 SODIUM ION × 12 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RLPMH_RHIJ3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 30–543； UniProt 1–514

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	9gvd
Deposition date deposition_date	2024-09-24
Last revision last_revision	2025-10-08
Structure title title	Structure of phosphonate monoester hydrolase from Rhizobium leguminosarum with vanadate
Keywords keywords	Phosphonate monoester hydrolase, promiscuous enzyme, 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.

9gvd__assembly_1__model_1

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

Download this curve (.dat)

9gvd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9gvd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.09 Å
Rg (electron density)	39.40 Å
Total Rg	39.76 Å
Atom count	16268
Residues	2044
Excluded volume	286850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9gvd__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 (5)

Entity 1 Entity 1 polymer

Description description	Multifunctional alkaline phosphatase superfamily protein pRL90232
Molecular weight formula_weight	61098.4 kDa
EC 编号 ec_number	3.1.4.-,3.1.3.-
Mutation mutation	C57fGly
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	4852

MASWSHPQFEKGAETAVPNSSSVPGDPSSMRKKNVLLIVVDQWRADFVPHVLRADGKIDFLKTPNLDRLCREGVTFRNHVTTCVPAGPARASLLTGLYLMNHRAVQNTVPLDQRHLNLGKALRGVGYDPALIGYTTTVPDPRTTSPNDPRFRVLGDLMDGFHPVGAFEPNMEGYFGWVAQNGFDLPEHRPDIWLPEGEDAVAGATDRPSRIPKEFSDSTFFTERALTYLKGRDGKPFFLHLGYYRPHPPFVASAPYHAMYRPEDMPAPIRAANPDIEAAQHPLMKFYVDSIRRGSFFQGAEGSGATLDEAELRQMRATYCGLITEVDDCLGRVFSYLDETGQWDDTLIIFTSDHGEQLGDHHLLGKIGYNDPSFRIPLVIKDAGENARAGAIESGFTESIDVMPTILDWLGGKIPHACDGLSLLPFLSEGRPQDWRTELHYEYDFRDVYYSEPQSFLGLGMNDCSLCVIQDERYKYVHFAALPPLFFDLRHDPNEFTNLADDPAYAALVRDYAQKALSWRLKHADRTLTHYRSGPEGLSERSH

Source Source

Source organism organism	Rhizobium johnstonii 3841
NCBI taxonomy ID ncbi_taxonomy_id	216596
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	VANADATE ION
Molecular weight formula_weight	114.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	727

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Unit-cell length a length_a	60.063 Å
Unit-cell length b length_b	97.129 Å
Unit-cell length c length_c	179.024 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	orthorhombic

Resolution resolution	1.200 Å
Low-resolution limit resolution_low	33.660 Å
R factor r_factor	0.1357
R_work r_work	0.1342
R_free r_free	0.1622

Structure of phosphonate monoester hydrolase from Rhizobium leguminosarum with vanadate

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

Multifunctional alkaline phosphatase superfamily protein pRL90232

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

9gvd__assembly_1__model_1

9gvd__assembly_1__model_1 | I(q)

9gvd__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Structure of phosphonate monoester hydrolase from Rhizobium leguminosarum with vanadate

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

Multifunctional alkaline phosphatase superfamily protein pRL90232

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

9gvd__assembly_1__model_1

9gvd__assembly_1__model_1 | I(q)

9gvd__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)