SAXSdb — 3dkq

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

PKHD-type hydroxylase Sbal_3634

Shewanella baltica OS155

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	NICKEL (II) ION × 6 IMIDAZOLE × 12 GLYCEROL × 12 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y3634_SHEB5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–243； UniProt 1–224 Author chain B； PDBConstruct 20–243； UniProt 1–224 Author chain C； PDBConstruct 20–243； UniProt 1–224

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	3dkq
Deposition date deposition_date	2008-06-25
Structure title title	Crystal structure of Putative Oxygenase (YP_001051978.1) from SHEWANELLA BALTICA OS155 at 2.26 A resolution
Keywords keywords	;YP_001051978.1, Putative Oxygenase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, Dioxygenase, Iron, Metal-binding, Oxidoreductase, Vitamin C ;; OXIDOREDUCTASE
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.

3dkq__assembly_1__model_1

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

Download this curve (.dat)

3dkq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dkq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.52 Å
Rg (electron density)	34.61 Å
Total Rg	34.81 Å
Atom count	10534
Residues	1286
Excluded volume	186790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dkq__assembly_1__model_1`	hexameric （6）	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	PKHD-type hydroxylase Sbal_3634
Molecular weight formula_weight	27978.3 kDa
EC 编号 ec_number	1.14.11.-
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5600

MGSDKIHHHHHHENLYFQGMLIEIPNVFSKQEVSHLREQLDARRWIDGNQTSGAMATTRKRNQQLDKDDPVAVALGQQIMDRLLAHPQFVSAALPLQFYPPLFNRYQGGETFGYHIDNAIRSTPDGMIRTDLSATLFLSEPENYQGGELVIQDTYGQQSIKLSAGSLVLYPSSSLHQVTPVLSGERTAAFMWLQSMVRDEGQRRLLFQLDQSIQSLTAQTAAEQELFNLSGVYHNLLRRWSEL

Source Source

Source organism organism	Shewanella baltica OS155
NCBI taxonomy ID ncbi_taxonomy_id	325240
Host organism host_organism	Escherichia Coli

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	244

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3dkqA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	620 — q2cbj1_9rhob like domain

Domain ID domain_id	3dkqA02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	860 — DNA Excision Repair, Uvrb; Chain A
Homologous superfamily homologous superfamily	20 — Rabenosyn, Rab binding domain

Domain ID domain_id	3dkqB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	620 — q2cbj1_9rhob like domain

Domain ID domain_id	3dkqB02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	860 — DNA Excision Repair, Uvrb; Chain A
Homologous superfamily homologous superfamily	20 — Rabenosyn, Rab binding domain

Domain ID domain_id	3dkqC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	620 — q2cbj1_9rhob like domain

Domain ID domain_id	3dkqC02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	860 — DNA Excision Repair, Uvrb; Chain A
Homologous superfamily homologous superfamily	20 — Rabenosyn, Rab binding domain

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Unit-cell length a length_a	153.452 Å
Unit-cell length b length_b	153.452 Å
Unit-cell length c length_c	84.851 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	24

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.260 Å
Low-resolution limit resolution_low	28.855 Å
R factor r_factor	0.1980
R_work r_work	0.1960
R_free r_free	0.2320

Crystal structure of Putative Oxygenase (YP_001051978.1) from SHEWANELLA BALTICA OS155 at 2.26 A resolution

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

PKHD-type hydroxylase Sbal_3634

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

3dkq__assembly_1__model_1

3dkq__assembly_1__model_1 | I(q)

3dkq__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

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of Putative Oxygenase (YP_001051978.1) from SHEWANELLA BALTICA OS155 at 2.26 A resolution

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

PKHD-type hydroxylase Sbal_3634

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

3dkq__assembly_1__model_1

3dkq__assembly_1__model_1 | I(q)

3dkq__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

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)