2a7k

carboxymethylproline synthase (CarB) from pectobacterium carotovora, apo enzyme

Method: X-RAY DIFFRACTION

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

CarB

Pectobacterium carotovorum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9XB60_ERWCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–250； UniProt 1–250 Author chain B； PDBConstruct 1–250； UniProt 1–250 Author chain C； PDBConstruct 1–250； UniProt 1–250 Author chain D； PDBConstruct 1–250； UniProt 1–250 Author chain E； PDBConstruct 1–250； UniProt 1–250 Author chain F； PDBConstruct 1–250； UniProt 1–250 Author chain G； PDBConstruct 1–250； UniProt 1–250 Author chain H； PDBConstruct 1–250； UniProt 1–250 Author chain I； PDBConstruct 1–250； UniProt 1–250

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	2a7k
Deposition date deposition_date	2005-07-05
Structure title title	carboxymethylproline synthase (CarB) from pectobacterium carotovora, apo enzyme
Keywords keywords	carbapenem, carbapenam, crotonase, antibiotic, beta-lactam, Biosynthetic Protein; BIOSYNTHETIC 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.

2a7k__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2a7k__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2a7k__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	27.15 Å
Rg (electron density)	25.76 Å
Total Rg	26.60 Å
Atom count	5295
Residues	690
Excluded volume	93716 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2a7k__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2a7k__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2a7k__assembly_3__model_1`	trimeric （3）	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 (2)

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6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2a7ka1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.3 — Crotonase-like

Domain ID domain_id	d2a7kb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.3 — Crotonase-like

Domain ID domain_id	d2a7kc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.3 — Crotonase-like

Domain ID domain_id	d2a7kd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.3 — Crotonase-like

Domain ID domain_id	d2a7ke_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.3 — Crotonase-like

Domain ID domain_id	d2a7kf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.3 — Crotonase-like

Domain ID domain_id	d2a7kg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.3 — Crotonase-like

Domain ID domain_id	d2a7kh_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.3 — Crotonase-like

Domain ID domain_id	d2a7ki_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.3 — Crotonase-like

CATH v4.4 (18 domains)

Domain ID domain_id	2a7kA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	2a7kA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	2a7kB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	2a7kB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	2a7kC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	2a7kC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	2a7kD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	2a7kD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	2a7kE01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	2a7kE02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	2a7kF01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	2a7kF02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	2a7kG01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	2a7kG02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	2a7kH01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	2a7kH02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	2a7kI01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	2a7kI02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1610 —

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Unit-cell length a length_a	87.207 Å
Unit-cell length b length_b	89.860 Å
Unit-cell length c length_c	264.582 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	36

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.240 Å
Low-resolution limit resolution_low	45.596 Å
R factor r_factor	0.1880
R_work r_work	0.1849
R_free r_free	0.2385

Description description	CarB
Molecular weight formula_weight	27608.3 kDa
Source method src_method	man
Copy count entity_count	9

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I
Atom count atom_count	16704

carboxymethylproline synthase (CarB) from pectobacterium carotovora, apo enzyme

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

CarB

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

2a7k__assembly_2__model_1

2a7k__assembly_2__model_1 | I(q)

2a7k__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (9 domains)

CATH v4.4 (18 domains)

7. Citations (1)

Source organism organism	Pectobacterium carotovorum
NCBI taxonomy ID ncbi_taxonomy_id	554
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	806

carboxymethylproline synthase (CarB) from pectobacterium carotovora, apo enzyme

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

CarB

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

2a7k__assembly_2__model_1

2a7k__assembly_2__model_1 | I(q)

2a7k__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (9 domains)

CATH v4.4 (18 domains)

7. Citations (1)