SAXSdb — 3b5j

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

Alpha-hemolysin translocation ATP-binding protein hlyB

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;2',3'-O-[(1R,6R)-2,4,6-trinitrocyclohexa-2,4-diene-1,1-diyl]adenosine 5'-(trihydrogen diphosphate) ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HLYBP_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–243； UniProt 467–707

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	3b5j
Deposition date deposition_date	2007-10-26
Structure title title	Crystal Structures of the S504A Mutant of an Isolated ABC-ATPase in Complex with TNP-ADP
Keywords keywords	;ABC-TRANSPORTER, NUCLEOTIDE-BINDING DOAMIN, ATPase, ATP-binding, Hydrolase, Inner membrane, Membrane, Transmembrane, TRANSPORT PROTEIN ;; TRANSPORT 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.

3b5j__assembly_1__model_1

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

Download this curve (.dat)

3b5j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3b5j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.09 Å
Rg (electron density)	18.85 Å
Total Rg	19.68 Å
Atom count	1953
Residues	243
Excluded volume	34671 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3b5j__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 (3)

Entity 1 Entity 1 polymer

Description description	Alpha-hemolysin translocation ATP-binding protein hlyB
Molecular weight formula_weight	27184.3 kDa
Mutation mutation	S504A
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	2214

HHDITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRAGSGKSTLTKLIQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLSTVKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;2',3'-O-[(1R,6R)-2,4,6-trinitrocyclohexa-2,4-diene-1,1-diyl]adenosine 5'-(trihydrogen diphosphate) ;
Molecular weight formula_weight	638.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	261

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3b5jA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	179.200 Å
Unit-cell length b length_b	34.600 Å
Unit-cell length c length_c	38.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.40 °
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	2.000 Å
Low-resolution limit resolution_low	17.980 Å
R factor r_factor	0.2090
R_work r_work	0.2040
R_free r_free	0.2800

Crystal Structures of the S504A Mutant of an Isolated ABC-ATPase in Complex with TNP-ADP

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

Alpha-hemolysin translocation ATP-binding protein hlyB

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

3b5j__assembly_1__model_1

3b5j__assembly_1__model_1 | I(q)

3b5j__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 (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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structures of the S504A Mutant of an Isolated ABC-ATPase in Complex with TNP-ADP

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

Alpha-hemolysin translocation ATP-binding protein hlyB

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

3b5j__assembly_1__model_1

3b5j__assembly_1__model_1 | I(q)

3b5j__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 (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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)