SAXSdb — 2w8s

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

PHOSPHONATE MONOESTER HYDROLASE

BURKHOLDERIA CARYOPHYLLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 4 FE (III) ION × 4 SULFATE ION × 7 GLYCEROL × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q45087_9BURK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 30–543； UniProt 1–514 Author chain B； PDBConstruct 30–543； UniProt 1–514 Author chain C； PDBConstruct 30–543； UniProt 1–514 Author chain D； 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	2w8s
Deposition date deposition_date	2009-01-19
Structure title title	CRYSTAL STRUCTURE OF A catalytically promiscuous PHOSPHONATE MONOESTER HYDROLASE FROM Burkholderia caryophylli
Keywords keywords	;HYDROLASE, FORMYLGLYCINE, PHOSPHODIESTERASE, ALKALINE PHOSPHATASE SUPERFAMILY, CATALYTIC PROMISCUITY, PHOSPHONATE MONOESTER 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.

2w8s__assembly_1__model_1

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

Download this curve (.dat)

2w8s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2w8s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.93 Å
Rg (electron density)	39.29 Å
Total Rg	39.61 Å
Atom count	16401
Residues	2047
Excluded volume	288070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2w8s__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 (6)

Entity 1 Entity 1 polymer

Description description	PHOSPHONATE MONOESTER HYDROLASE
Molecular weight formula_weight	61220.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	17251

MASWSHPQFEKGAETAVPNSSSVPGDPSSMTRKNVLLIVVDQWRADFIPHLMRAEGREPFLKTPNLDRLCREGLTFRNHVTTCVPGGPARASLLTGLYLMNHRAVQNTVPLDQRHLNLGKALRAIGYDPALIGYTTTTPDPRTTSARDPRFTVLGDIMDGFRSVGAFEPNMEGYFGWVAQNGFELPENREDIWLPEGEHSVPGATDKPSRIPKEFSDSTFFTERALTYLKGRDGKPFFLHLGYYRPHPPFVASAPYHAMYKAEDMPAPIRAENPDAEAAQHPLMKHYIDHIRRGSFFHGAEGSGATLDEGEIRQMRATYCGLITEIDDCLGRVFAYLDETGQWDDTLIIFTSDHGEQLGDHHLLGKIGYNAESFRIPLVIKDAGQNRHAGQIEEGFSESIDVMPTILEWLGGETPRACDGRSLLPFLAEGKPSDWRTELHYEFDFRDVFYDQPQNSVQLSQDDCSLCVIEDENYKYVHFAALPPLFFDLKADPHEFSNLAGDPAYAALVRDYAQKALSWRLSHADRTLTHYRSSPQGLTTRNH

Source Source

Source organism organism	BURKHOLDERIA CARYOPHYLLI
NCBI taxonomy ID ncbi_taxonomy_id	28094
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	818

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2w8sA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	720 — Alkaline Phosphatase, subunit A
Homologous superfamily homologous superfamily	10 — Alkaline Phosphatase, subunit A

Domain ID domain_id	2w8sA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3360 —

Domain ID domain_id	2w8sB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	720 — Alkaline Phosphatase, subunit A
Homologous superfamily homologous superfamily	10 — Alkaline Phosphatase, subunit A

Domain ID domain_id	2w8sB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3360 —

Domain ID domain_id	2w8sC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	720 — Alkaline Phosphatase, subunit A
Homologous superfamily homologous superfamily	10 — Alkaline Phosphatase, subunit A

Domain ID domain_id	2w8sC02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3360 —

Domain ID domain_id	2w8sD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	720 — Alkaline Phosphatase, subunit A
Homologous superfamily homologous superfamily	10 — Alkaline Phosphatase, subunit A

Domain ID domain_id	2w8sD02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3360 —

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Unit-cell length a length_a	57.700 Å
Unit-cell length b length_b	200.100 Å
Unit-cell length c length_c	211.700 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	48.620 Å
R factor r_factor	0.1850
R_work r_work	0.1820
R_free r_free	0.2390

CRYSTAL STRUCTURE OF A catalytically promiscuous PHOSPHONATE MONOESTER HYDROLASE FROM Burkholderia caryophylli

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

PHOSPHONATE MONOESTER HYDROLASE

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

2w8s__assembly_1__model_1

2w8s__assembly_1__model_1 | I(q)

2w8s__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (2)

CRYSTAL STRUCTURE OF A catalytically promiscuous PHOSPHONATE MONOESTER HYDROLASE FROM Burkholderia caryophylli

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

PHOSPHONATE MONOESTER HYDROLASE

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

2w8s__assembly_1__model_1

2w8s__assembly_1__model_1 | I(q)

2w8s__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (2)