SAXSdb — 5fjo

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

N-succinylamino acid racemase

Amycolatopsis sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	N-acetyl naphthylalanine × 8 MAGNESIUM ION × 8 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NSAR_AMYSP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–368； UniProt 1–368 Author chain B； PDBConstruct 1–368； UniProt 1–368

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	5fjo
Deposition date deposition_date	2015-10-12
Structure title title	N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: G291D- F323Y mutant in complex with N-acetyl naphthylalanine
Keywords keywords	LYASE, RACEMASE, ACYL AMINO ACID, ISOMERASE, AMYCOLATOPSIS; LYASE
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.

5fjo__assembly_1__model_1

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

Download this curve (.dat)

5fjo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5fjo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.60 Å
Rg (electron density)	42.00 Å
Total Rg	42.35 Å
Atom count	22344
Residues	2940
Excluded volume	400120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5fjo__assembly_1__model_1`	octameric （8）	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	N-succinylamino acid racemase
Molecular weight formula_weight	39522.3 kDa
EC 编号 ec_number	5.1.1.-,4.2.1.113
Mutation mutation	YES
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	6463

MKLSGVELRRVQMPLVAPFRTSFGTQSVRELLLLRAVTPAGEGWGECVTMAGPLYSSEYNDGAEHVLRHYLIPALLAAEDITAAKVTPLLAKFKGHRMAKGALEMAVLDAELRAHERSFAAELGSVRDSVPCGVSVGIMDTIPQLLDVVGGYLDEGYVRIKLKIEPGWDVEPVRAVRERFGDDVLLQVDANTAYTLGDAPQLARLDPFGLLLIEQPLEEEDVLGHAELARRIQTPICLDESIVSARAAADAIKLGAVQIVNIKPGRVGGYLEARRVHDVCAAHGIPVWCGDMIETGLGRAANVALASLPNFTLPGDTSASDRYYKTDITEPFVLSGGHLPVPTGPGLGVAPIPELLDEVTTAKVWIGS

Source Source

Source organism organism	Amycolatopsis sp.
NCBI taxonomy ID ncbi_taxonomy_id	37632
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	N-acetyl naphthylalanine
Molecular weight formula_weight	257.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	877

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5fjoa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
Family Family family	d.54.1.0 — automated matches

Domain ID domain_id	d5fjoa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
Family Family family	c.1.11.2 — D-glucarate dehydratase-like

Domain ID domain_id	d5fjob1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
Family Family family	d.54.1.0 — automated matches

Domain ID domain_id	d5fjob2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
Family Family family	c.1.11.2 — D-glucarate dehydratase-like

CATH v4.4 (4 domains)

Domain ID domain_id	5fjoA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

Domain ID domain_id	5fjoA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	120 — Enolase-like C-terminal domain

Domain ID domain_id	5fjoB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

Domain ID domain_id	5fjoB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	120 — Enolase-like C-terminal domain

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Unit-cell length a length_a	164.710 Å
Unit-cell length b length_b	164.710 Å
Unit-cell length c length_c	169.590 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	32

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	68.550 Å
R factor r_factor	0.1461
R_work r_work	0.1446
R_free r_free	0.1746

N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: G291D- F323Y mutant in complex with N-acetyl naphthylalanine

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

N-succinylamino acid racemase

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

5fjo__assembly_1__model_1

5fjo__assembly_1__model_1 | I(q)

5fjo__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: G291D- F323Y mutant in complex with N-acetyl naphthylalanine

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

N-succinylamino acid racemase

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

5fjo__assembly_1__model_1

5fjo__assembly_1__model_1 | I(q)

5fjo__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)