SAXSdb — 3chv

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

Prokaryotic domain of unknown function (DUF849) with a TIM barrel fold

Silicibacter pomeroyi DSS-3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 CHLORIDE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5LLI5_SILPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–284； UniProt 1–283

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	3chv
Deposition date deposition_date	2008-03-10
Structure title title	CRYSTAL STRUCTURE OF a prokaryotic domain of unknown function (DUF849) member (SPOA0042) FROM SILICIBACTER POMEROYI DSS-3 AT 1.45 A RESOLUTION
Keywords keywords	;TIM BARREL FOLD, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, METAL BINDING PROTEIN ;; METAL BINDING PROTEIN
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.

3chv__assembly_1__model_1

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

Download this curve (.dat)

3chv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3chv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.71 Å
Rg (electron density)	25.12 Å
Total Rg	25.70 Å
Atom count	4192
Residues	540
Excluded volume	74301 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3chv__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 (4)

Entity 1 Entity 1 polymer

Description description	Prokaryotic domain of unknown function (DUF849) with a TIM barrel fold
Molecular weight formula_weight	31347.0 kDa
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	2636

GMDTPANKPCIICVAITGSVPTKADNPAVPITVSEQVESTQEAFEAGAAIAHCHVRNDDGTPSSDPDRFARLTEGLHTHCPGMIVQFSTGGRSGAGQARGGMLPLKPDMASLSVGSNNFPSRVYENPPDLVDWLAAQMRSYRVTPEIEAFDLSHILRAIDMHGRGLLYGKLYVQFVMGVKNAMPADREVFDFYVRMMRTRAPQAEWCAAGIGANQLTVNEWAIAAGGHTRTGLEDNIRLDRQTLAPSNAALVRRSVELCDKYQRPVASWQQAREILGLPAAARN

Source Source

Source organism organism	Silicibacter pomeroyi DSS-3
NCBI taxonomy ID ncbi_taxonomy_id	246200
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	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	367

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3chvA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	68.859 Å
Unit-cell length b length_b	69.601 Å
Unit-cell length c length_c	52.331 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.19 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	29.696 Å
R factor r_factor	0.1340
R_work r_work	0.1330
R_free r_free	0.1580

CRYSTAL STRUCTURE OF a prokaryotic domain of unknown function (DUF849) member (SPOA0042) FROM SILICIBACTER POMEROYI DSS-3 AT 1.45 A RESOLUTION

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

Prokaryotic domain of unknown function (DUF849) with a TIM barrel fold

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

3chv__assembly_1__model_1

3chv__assembly_1__model_1 | I(q)

3chv__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF a prokaryotic domain of unknown function (DUF849) member (SPOA0042) FROM SILICIBACTER POMEROYI DSS-3 AT 1.45 A RESOLUTION

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

Prokaryotic domain of unknown function (DUF849) with a TIM barrel fold

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

3chv__assembly_1__model_1

3chv__assembly_1__model_1 | I(q)

3chv__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)