SAXSdb — 3di4

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

Uncharacterized Protein DUF1989

Silicibacter pomeroyi

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 × 2 CHLORIDE ION × 4 GLYCEROL × 1 SULFATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5LXE3_SILPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–286； UniProt 1–285 Author chain B； PDBConstruct 2–286； UniProt 1–285

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	3di4
Deposition date deposition_date	2008-06-19
Structure title title	Crystal structure of a duf1989 family protein (spo0365) from silicibacter pomeroyi dss-3 at 1.60 A resolution
Keywords keywords	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.

3di4__assembly_1__model_1

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

Download this curve (.dat)

3di4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3di4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.74 Å
Rg (electron density)	22.86 Å
Total Rg	23.66 Å
Atom count	4262
Residues	544
Excluded volume	75004 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3di4__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 (6)

Entity 1 Entity 1 polymer

Description description	Uncharacterized Protein DUF1989
Molecular weight formula_weight	31597.5 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	5100

GMTDAPADAPLDADARRAVKPVICYPNDSLPRPDLALYRAARASARKTGEVLVPPREGRCFEVKAGQFFRISSVEGPQVGDLNLHNLHDLTERFFSGKTRALHGTHVTTGERLWSNLPYLRPMATIIEDTLGWYGIDQYGGSVHDVIGTRCDPYTGNLLAGGHYHHCCHSNLTRALADHTGLPLHEAEMLVHDVLNVFMCTGFTRDTGQYFMKASPVRPGDYLEFFAEIDLLGNLSACPGGDCSSEHSSDTASCHPLLVEIFAPAEGMLGDWPSPSVNGYDRSHGR

Source Source

Source organism organism	Silicibacter pomeroyi
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	4

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	1

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	739

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Unit-cell length a length_a	51.465 Å
Unit-cell length b length_b	95.764 Å
Unit-cell length c length_c	58.689 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.04 °
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	1.600 Å
Low-resolution limit resolution_low	28.410 Å
R factor r_factor	0.1420
R_work r_work	0.1410
R_free r_free	0.1750

Crystal structure of a duf1989 family protein (spo0365) from silicibacter pomeroyi dss-3 at 1.60 A resolution

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

Uncharacterized Protein DUF1989

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

3di4__assembly_1__model_1

3di4__assembly_1__model_1 | I(q)

3di4__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

7. Citations (1)

Crystal structure of a duf1989 family protein (spo0365) from silicibacter pomeroyi dss-3 at 1.60 A resolution

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

Uncharacterized Protein DUF1989

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

3di4__assembly_1__model_1

3di4__assembly_1__model_1 | I(q)

3di4__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

7. Citations (1)