4djd

Crystal structure of folate-free corrinoid iron-sulfur protein (CFeSP) in complex with its methyltransferase (MeTr)

Method: X-RAY DIFFRACTION

▼

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

5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase

Moorella thermoacetica

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Corrinoid/iron-sulfur protein large subunit × 2 （Q07340） Corrinoid/iron-sulfur protein small subunit × 2 （Q07341） CALCIUM ION × 2 IRON/SULFUR CLUSTER × 2 COBALAMIN × 2 GLYCEROL × 10 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q46389_MOOTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–262； UniProt 1–262 Author chain B； PDBConstruct 1–262； UniProt 1–262

Corrinoid/iron-sulfur protein large subunit

OrganismNot specified

UniProt Q07340

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase × 2 （Q46389） Corrinoid/iron-sulfur protein small subunit × 2 （Q07341） CALCIUM ION × 2 IRON/SULFUR CLUSTER × 2 COBALAMIN × 2 GLYCEROL × 10 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACSC_MOOTH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–446； UniProt 1–446 Author chain E； PDBConstruct 1–446； UniProt 1–446

Corrinoid/iron-sulfur protein small subunit

OrganismNot specified

UniProt Q07341

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase × 2 （Q46389） Corrinoid/iron-sulfur protein large subunit × 2 （Q07340） CALCIUM ION × 2 IRON/SULFUR CLUSTER × 2 COBALAMIN × 2 GLYCEROL × 10 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACSD_MOOTH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–323； UniProt 1–323 Author chain F； PDBConstruct 1–323； UniProt 1–323

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4djd
Deposition date deposition_date	2012-02-01
Structure title title	Crystal structure of folate-free corrinoid iron-sulfur protein (CFeSP) in complex with its methyltransferase (MeTr)
Keywords keywords	TIM barrel, Rossmann fold, B12-dependent methyltransferase, TRANSFERASE-VITAMIN-BINDING PROTEIN complex; TRANSFERASE/VITAMIN-BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4djd__assembly_1__model_1

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

Download this curve (.dat)

4djd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4djd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.99 Å
Rg (electron density)	42.56 Å
Total Rg	42.50 Å
Atom count	15422
Residues	2052
Excluded volume	274770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4djd__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase
Molecular weight formula_weight	28638.1 kDa
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	15832

MLIIGERINGMFGDIKRAIQERDPAPVQEWARRQEEGGARALDLNVGPAVQDKVSAMEWLVEVTQEVSNLTLCLDSTNIKAIEAGLKKCKNRAMINSTNAEREKVEKLFPLAVEHGAALIGLTMNKTGIPKDSDTRLAFAMELVAAADEFGLPMEDLYIDPLILPANVAQDHAPEVLKTLQQIKMLADPAPKTVLGLSNVSQNCQNRPLINRTFLAMAMACGLDAAIADACDEALIETAATAEILLNQTVYCDSFVKMFKTR

Source Source

Source organism organism	Moorella thermoacetica
NCBI taxonomy ID ncbi_taxonomy_id	1525
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Corrinoid/iron-sulfur protein large subunit
Molecular weight formula_weight	48207.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,E

MPLTGLEIYKQLPKKNCGECGTPTCLAFAMNLASGKASLDSCPYVSDAAREALDAAAAPPIAKVVLGAGPTAVEMGDETELFRHDKRFYHETAIAIQVSDNLSSEELKAKVEAINGLNFDRVGQHYTIQAIAIRHDADDPAAFKAAVASVAAATQLNLVLMADDPDVLKEALAGVADRKPLLYAATGANYEAMTALAKENNCPLAVYGNGLEELAELVDKIVALGHKQLVLDPGARETSRAIADFTQIRRLAIKKRFRSFGYPIIALTTAANPLDEVLQAVNYVTKYASLVVLRTDAKEHLLPLLSWRQNLYTDPQVPIRVEEKLNEIGAVNENSPVYVTTNFSLTYYSVEGEIESTKIPSYLLSVDTDGLSVLTAYADGKFEAEKIAAVMKKVDLDNKVKRHRIIIPGAVAVLKGKLEDLTGWEVIVGPREASGIVAFARANLAS

Entity 3 Entity 3 polymer

Description description	Corrinoid/iron-sulfur protein small subunit
Molecular weight formula_weight	35107.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F

MAVQILRDRSRAAVQKVVLGATKDQGGTRSHTIVVGGDAALPFHHFEGEIVNRPVIGMEVQDIVPDWPDVLKDPFTDVINEPGRWAQKCVAEYGADLIYLKLDGADPEGANHSVDQCVATVKEVLQAVGVPLVVVGCGDVEKDHEVLEAVAEAAAGENLLLGNAEQENYKSLTAACMVHKHNIIARSPLDINICKQLNILINEMNLPLDHIVIDPSIGGLGYGIEYSFSIMERIRLGALQGDKMLSMPVICTVGYEAWRAKEASAPVSEYPGWGKETERGILWEAVTATALLQAGAHILLMRHPEAVARVKENIDQLMVSNAY

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	COBALAMIN
Molecular weight formula_weight	1330.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	401

▼

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4djda_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.21 — Dihydropteroate synthetase-like
Family Family family	c.1.21.2 — Methyltetrahydrofolate-utiluzing methyltransferases

Domain ID domain_id	d4djdb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.21 — Dihydropteroate synthetase-like
Family Family family	c.1.21.2 — Methyltetrahydrofolate-utiluzing methyltransferases

CATH v4.4 (8 domains)

Domain ID domain_id	4djdA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	20 — Dihydropteroate synthase-like

Domain ID domain_id	4djdB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	20 — Dihydropteroate synthase-like

Domain ID domain_id	4djdC01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	20 — Dihydropteroate synthase-like

Domain ID domain_id	4djdC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11600 —

Domain ID domain_id	4djdD01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	20 — Dihydropteroate synthase-like

Domain ID domain_id	4djdE01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	20 — Dihydropteroate synthase-like

Domain ID domain_id	4djdE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11600 —

Domain ID domain_id	4djdF01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	20 — Dihydropteroate synthase-like

▶

Unit-cell length a length_a	125.614 Å
Unit-cell length b length_b	242.843 Å
Unit-cell length c length_c	79.665 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.380 Å
Low-resolution limit resolution_low	39.833 Å
R factor r_factor	0.1891
R_work r_work	0.1869
R_free r_free	0.2287

Crystal structure of folate-free corrinoid iron-sulfur protein (CFeSP) in complex with its methyltransferase (MeTr)

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

5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Corrinoid/iron-sulfur protein large subunit

State in the Current Structure

Other States of the Same Protein in the Database

Corrinoid/iron-sulfur protein small subunit

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

4djd__assembly_1__model_1

4djd__assembly_1__model_1 | I(q)

4djd__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of folate-free corrinoid iron-sulfur protein (CFeSP) in complex with its methyltransferase (MeTr)

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

5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Corrinoid/iron-sulfur protein large subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Corrinoid/iron-sulfur protein small subunit

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

4djd__assembly_1__model_1

4djd__assembly_1__model_1 | I(q)

4djd__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

CATH v4.4 (8 domains)

7. Citations (1)