SAXSdb — 2afv

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

cobalamin biosynthesis precorrin isomerase

Leptospira interrogans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 8 HEXAETHYLENE GLYCOL × 1 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	CHLORIDE ION × 16 HEXAETHYLENE GLYCOL × 2 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8EXP7_LEPIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–223； UniProt 1–223 Author chain B； PDBConstruct 1–223； UniProt 1–223

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	2afv
Deposition date deposition_date	2005-07-26
Structure title title	The Crystal Structure of Putative Precorrin Isomerase CbiC in Cobalamin Biosynthesis
Keywords keywords	ISOMERASE; ISOMERASE
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.

2afv__assembly_1__model_1

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

Download this curve (.dat)

2afv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2afv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.75 Å
Rg (electron density)	21.61 Å
Total Rg	22.42 Å
Atom count	3333
Residues	434
Excluded volume	60247 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2afv__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2afv__assembly_2__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	cobalamin biosynthesis precorrin isomerase
Molecular weight formula_weight	25887.9 kDa
EC 编号 ec_number	5.4.1.2
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	3396

MNDMRQITNLGRNIENKSFSIIDEEAGPHSFAQEEWEVVRRIIHATADFDYKNITKIHPQAIDSGIQALKKGCPIVCDVQMILSGLNPERLKVYGCKTYCFISDEDVIENAKRKNSTRAIESIQKANSFNLLNESIIVIGNAPTALLEIEKLIRQEGIKPALIVGVPVGFVSAKESKESILKLEYYNVTSIPYILTMGRKGGSTIAVAILHALLLLSSKRGERLEHHHHHH

Source Source

Source organism organism	Leptospira interrogans
NCBI taxonomy ID ncbi_taxonomy_id	173
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	HEXAETHYLENE GLYCOL
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
Molecular weight formula_weight	326.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	63

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2afvA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10230 — Cobalamin biosynthesis CobH/CbiC, precorrin-8X methylmutase

Domain ID domain_id	2afvB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10230 — Cobalamin biosynthesis CobH/CbiC, precorrin-8X methylmutase

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Unit-cell length a length_a	113.078 Å
Unit-cell length b length_b	113.078 Å
Unit-cell length c length_c	114.502 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	16

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	19.870 Å
R factor r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2510

The Crystal Structure of Putative Precorrin Isomerase CbiC in Cobalamin Biosynthesis

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

cobalamin biosynthesis precorrin isomerase

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

2afv__assembly_1__model_1

2afv__assembly_1__model_1 | I(q)

2afv__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

The Crystal Structure of Putative Precorrin Isomerase CbiC in Cobalamin Biosynthesis

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

cobalamin biosynthesis precorrin isomerase

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

2afv__assembly_1__model_1

2afv__assembly_1__model_1 | I(q)

2afv__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)