SAXSdb — 1vjf

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

DNA-binding protein, putative

Caulobacter crescentus CB15

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 GLYCEROL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9ABV9_CAUCR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–180； UniProt 1–168

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	1vjf
Deposition date deposition_date	2004-02-11
Structure title title	CRYSTAL STRUCTURE OF A PUTATIVE DNA-BINDING PROTEIN (CC_0111) FROM CAULOBACTER CRESCENTUS CB15 AT 1.62 A RESOLUTION
Keywords keywords	DNA BINDING PROTEIN, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI; DNA 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.

1vjf__assembly_1__model_1

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

Download this curve (.dat)

1vjf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vjf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.61 Å
Rg (electron density)	15.25 Å
Total Rg	16.39 Å
Atom count	1283
Residues	162
Excluded volume	23122 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vjf__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	DNA-binding protein, putative
Molecular weight formula_weight	20031.1 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	1501

MGSDKIHHHHHHMKTRADLFAFFDAHGVDHKTLDHPPVFRVEEGLEIKAAMPGGHTKNLFLKDAKGQLWLISALGETTIDLKKLHHVIGSGRLSFGPQEMMLETLGVTPGSVTAFGLINDTEKRVRFVLDKALADSDPVNFHPLKNDATTAVSQAGLRRFLAALGVEPMIVDFAAMEVVG

Source Source

Source organism organism	Caulobacter crescentus CB15
NCBI taxonomy ID ncbi_taxonomy_id	190650
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	172

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1vjfa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.116 — YbaK/ProRS associated domain
Superfamily Superfamily superfamily	d.116.1 — YbaK/ProRS associated domain
Family Family family	d.116.1.1 — YbaK/ProRS associated domain

CATH v4.4 (1 domains)

Domain ID domain_id	1vjfA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	960 — YbaK protein
Homologous superfamily homologous superfamily	10 — YbaK/aminoacyl-tRNA synthetase-associated domain

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Unit-cell length a length_a	50.891 Å
Unit-cell length b length_b	50.891 Å
Unit-cell length c length_c	121.430 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.620 Å
Low-resolution limit resolution_low	46.940 Å
R factor r_factor	0.1460
R_work r_work	0.1449
R_free r_free	0.1667

CRYSTAL STRUCTURE OF A PUTATIVE DNA-BINDING PROTEIN (CC_0111) FROM CAULOBACTER CRESCENTUS CB15 AT 1.62 A RESOLUTION

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

DNA-binding protein, putative

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

1vjf__assembly_1__model_1

1vjf__assembly_1__model_1 | I(q)

1vjf__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF A PUTATIVE DNA-BINDING PROTEIN (CC_0111) FROM CAULOBACTER CRESCENTUS CB15 AT 1.62 A RESOLUTION

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

DNA-binding protein, putative

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

1vjf__assembly_1__model_1

1vjf__assembly_1__model_1 | I(q)

1vjf__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)