SAXSdb — 5t4t

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

Fluoroacetate dehalogenase

Rhodopseudomonas palustris

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DEHA_RHOPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–304； UniProt 1–302 Author chain B； PDBConstruct 3–304； UniProt 1–302

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	5t4t
Deposition date deposition_date	2016-08-30
Structure title title	Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn - Apo No Halide
Keywords keywords	Homodimer, Hydrolase, Dehalogenase; HYDROLASE
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.

5t4t__assembly_1__model_1

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

Download this curve (.dat)

5t4t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5t4t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.53 Å
Rg (electron density)	26.93 Å
Total Rg	27.66 Å
Atom count	4713
Residues	596
Excluded volume	83435 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5t4t__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 (3)

Entity 1 Entity 1 polymer

Description description	Fluoroacetate dehalogenase
Molecular weight formula_weight	34072.7 kDa
EC 编号 ec_number	3.8.1.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	5398

GHMPDLADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHNRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASGIAQSAATPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSAAPGS

Source Source

Source organism organism	Rhodopseudomonas palustris
NCBI taxonomy ID ncbi_taxonomy_id	1076
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	659

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5t4ta1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d5t4ta2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5t4tb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5t4tA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	5t4tB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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Unit-cell length a length_a	41.880 Å
Unit-cell length b length_b	78.850 Å
Unit-cell length c length_c	85.130 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.71 °
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	1.511 Å
Low-resolution limit resolution_low	82.704 Å
R factor r_factor	0.1690
R_work r_work	0.1671
R_free r_free	0.2037

Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn - Apo No Halide

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

Fluoroacetate dehalogenase

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

5t4t__assembly_1__model_1

5t4t__assembly_1__model_1 | I(q)

5t4t__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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn - Apo No Halide

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

Fluoroacetate dehalogenase

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

5t4t__assembly_1__model_1

5t4t__assembly_1__model_1 | I(q)

5t4t__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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)