SAXSdb — 4oj8

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

(5R)-carbapenem-3-carboxylate synthase

Pectobacterium carotovorum subsp. carotovorum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	FE (II) ION × 6 2-OXOGLUTARIC ACID × 6 GLYCEROL × 2 (2S,5S)-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic acid × 4 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CARC_PECCC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–293； UniProt 1–273 Author chain B； PDBConstruct 21–293； UniProt 1–273 Author chain C； PDBConstruct 21–293； UniProt 1–273

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	4oj8
Deposition date deposition_date	2014-01-20
Structure title title	Crystal structure of carbapenem synthase in complex with (3S,5S)-carbapenam
Keywords keywords	oxidoreductase, oxygenase, iron, 2-oxoglutaric acid, antibiotic biosynthesis, carbapenam; OXIDOREDUCTASE
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.

4oj8__assembly_1__model_1

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

Download this curve (.dat)

4oj8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4oj8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.24 Å
Rg (electron density)	35.03 Å
Total Rg	35.62 Å
Atom count	13160
Residues	1590
Excluded volume	233810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4oj8__assembly_1__model_1`	hexameric （6）	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 (6)

Entity 1 Entity 1 polymer

Description description	(5R)-carbapenem-3-carboxylate synthase
Molecular weight formula_weight	33821.2 kDa
EC 编号 ec_number	1.14.20.3
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6991

MGSSHHHHHHSSGLVPRGSHMSEIVKFNPVMASGFGAYIDHRDFLEAKTETIKNLLMRQGFVVVKNLDIDSDTFRDIYSAYGTIVEYADEKIGVGFGYRDTLKLEGEKGKIVTGRGQLPFHADGGLLLSQVDQVFLYAAEIKNVKFRGATTVCDHALACQEMPAHLLRVLEEETFEVRVLERGYYVDVSPDGWFKVPVFTDLGWVRKMLIYFPFDEGQPASWEPRIVGFTDHETQAFFQELGAFLKQPRYYYKHFWEDGDLLIMDNRRVIHEREEFNDDDIVRRLYRGQTADI

Source Source

Source organism organism	Pectobacterium carotovorum subsp. carotovorum
NCBI taxonomy ID ncbi_taxonomy_id	555
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	2-OXOGLUTARIC ACID
Molecular weight formula_weight	146.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	(2S,5S)-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
Molecular weight formula_weight	155.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	411

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4oj8a1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.8 — gamma-Butyrobetaine hydroxylase

Domain ID domain_id	d4oj8a2
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	d4oj8b1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.8 — gamma-Butyrobetaine hydroxylase

Domain ID domain_id	d4oj8b2
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	d4oj8c1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.8 — gamma-Butyrobetaine hydroxylase

Domain ID domain_id	d4oj8c2
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

CATH v4.4 (3 domains)

Domain ID domain_id	4oj8A00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	130 — Double-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Clavaminate synthase-like

Domain ID domain_id	4oj8B00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	130 — Double-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Clavaminate synthase-like

Domain ID domain_id	4oj8C00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	130 — Double-stranded beta-helix
Homologous superfamily homologous superfamily	10 — Clavaminate synthase-like

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Unit-cell length a length_a	80.251 Å
Unit-cell length b length_b	165.778 Å
Unit-cell length c length_c	146.580 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	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2001
R_work r_work	0.1983
R_free r_free	0.2357

Crystal structure of carbapenem synthase in complex with (3S,5S)-carbapenam

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

(5R)-carbapenem-3-carboxylate synthase

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

4oj8__assembly_1__model_1

4oj8__assembly_1__model_1 | I(q)

4oj8__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of carbapenem synthase in complex with (3S,5S)-carbapenam

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

(5R)-carbapenem-3-carboxylate synthase

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

4oj8__assembly_1__model_1

4oj8__assembly_1__model_1 | I(q)

4oj8__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)