SAXSdb — 3djm

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

Uncharacterized Protein DUF427

Rhodobacter sphaeroides 2.4.1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3J512_RHOS4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–116； UniProt 1–115 Author chain B； PDBConstruct 2–116； UniProt 1–115 Author chain C； PDBConstruct 2–116； UniProt 1–115 Author chain D； PDBConstruct 2–116； UniProt 1–115 Author chain E； PDBConstruct 2–116； UniProt 1–115

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	3djm
Deposition date deposition_date	2008-06-23
Structure title title	CRYSTAL STRUCTURE OF A PROTEIN OF UNKNOWN FUNCTION FROM DUF427 FAMILY (RSPH17029_0682) FROM RHODOBACTER SPHAEROIDES 2.4.1 AT 2.51 A RESOLUTION
Keywords keywords	STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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.

3djm__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3djm__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3djm__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	14.80 Å
Rg (electron density)	13.36 Å
Total Rg	14.76 Å
Atom count	843
Residues	108
Excluded volume	15118 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3djm__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3djm__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3djm__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3djm__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3djm__assembly_5__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	Uncharacterized Protein DUF427
Molecular weight formula_weight	12928.0 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	4469

GMQMNNHIRLRKAEGKWVIRTDSAVLGETLNAIELTEGSRDPVIYFPREDVAMVMFDKSEKVTACPLKGEASYYSIVGASGTLKDAAWSYESPKEGLEAIAGYLAFAPDCTKVGQY

Source Source

Source organism organism	Rhodobacter sphaeroides 2.4.1
NCBI taxonomy ID ncbi_taxonomy_id	272943
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	153

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	3djmA00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	40 — Domain of unknown function (DUF427)

Domain ID domain_id	3djmB00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	40 — Domain of unknown function (DUF427)

Domain ID domain_id	3djmC00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	40 — Domain of unknown function (DUF427)

Domain ID domain_id	3djmD00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	40 — Domain of unknown function (DUF427)

Domain ID domain_id	3djmE00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	40 — Domain of unknown function (DUF427)

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Unit-cell length a length_a	66.403 Å
Unit-cell length b length_b	93.087 Å
Unit-cell length c length_c	128.016 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	20

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

Resolution resolution	2.510 Å
Low-resolution limit resolution_low	28.831 Å
R factor r_factor	0.2130
R_work r_work	0.2120
R_free r_free	0.2280

CRYSTAL STRUCTURE OF A PROTEIN OF UNKNOWN FUNCTION FROM DUF427 FAMILY (RSPH17029_0682) FROM RHODOBACTER SPHAEROIDES 2.4.1 AT 2.51 A RESOLUTION

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

Uncharacterized Protein DUF427

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

3djm__assembly_3__model_1

3djm__assembly_3__model_1 | I(q)

3djm__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF A PROTEIN OF UNKNOWN FUNCTION FROM DUF427 FAMILY (RSPH17029_0682) FROM RHODOBACTER SPHAEROIDES 2.4.1 AT 2.51 A RESOLUTION

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

Uncharacterized Protein DUF427

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

3djm__assembly_3__model_1

3djm__assembly_3__model_1 | I(q)

3djm__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)