3e05

CRYSTAL STRUCTURE OF Precorrin-6y C5,15-methyltransferase FROM Geobacter metallireducens GS-15

Method: X-RAY DIFFRACTION

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

Precorrin-6Y C5,15-methyltransferase (Decarboxylating)

Geobacter metallireducens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	CHLORIDE ION × 4 GLYCEROL × 1 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	CHLORIDE ION × 4 GLYCEROL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q39YF0_GEOMG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–197； UniProt 211–405 Author chain B； PDBConstruct 3–197； UniProt 211–405 Author chain C； PDBConstruct 3–197； UniProt 211–405 Author chain D； PDBConstruct 3–197； UniProt 211–405 Author chain E； PDBConstruct 3–197； UniProt 211–405 Author chain F； PDBConstruct 3–197； UniProt 211–405 Author chain G； PDBConstruct 3–197； UniProt 211–405 Author chain H； PDBConstruct 3–197； UniProt 211–405

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	3e05
Deposition date deposition_date	2008-07-30
Structure title title	CRYSTAL STRUCTURE OF Precorrin-6y C5,15-methyltransferase FROM Geobacter metallireducens GS-15
Keywords keywords	;Porphyrin METABOLISM, S-ADENOSYL-METHIONINE, STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, PSI, NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM, NYSGXRC, METHYLTRANSFERASE, DECARBOXYLASE, Transferase, New York SGX Research Center for Structural Genomics ;; TRANSFERASE
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.

3e05__assembly_2__model_1

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

Download this curve (.dat)

3e05__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3e05__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.91 Å
Rg (electron density)	27.59 Å
Total Rg	28.35 Å
Atom count	5911
Residues	760
Excluded volume	106110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3e05__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3e05__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 (4)

Entity 1 Entity 1 polymer

Description description	Precorrin-6Y C5,15-methyltransferase (Decarboxylating)
Molecular weight formula_weight	22733.9 kDa
EC 编号 ec_number	2.1.1.132
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	12584

MSLAQYPVIGIDDDEFATAKKLITKQEVRAVTLSKLRLQDDLVMWDIGAGSASVSIEASNLMPNGRIFALERNPQYLGFIRDNLKKFVARNVTLVEAFAPEGLDDLPDPDRVFIGGSGGMLEEIIDAVDRRLKSEGVIVLNAVTLDTLTKAVEFLEDHGYMVEVACVNVAKTKGLTEYKMFESHNPVYIITAWKSDEGHHHHHH

Source Source

Source organism organism	Geobacter metallireducens
NCBI taxonomy ID ncbi_taxonomy_id	269799
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	GLYCEROL
Molecular weight formula_weight	92.1 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	537

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3e05a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d3e05b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d3e05c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d3e05d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d3e05e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d3e05f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d3e05g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d3e05h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	3e05A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	3e05B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	3e05C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	3e05D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	3e05E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	3e05F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	3e05G00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	3e05H00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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Unit-cell length a length_a	124.710 Å
Unit-cell length b length_b	83.451 Å
Unit-cell length c length_c	149.056 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.72 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2171
R_work r_work	0.2157
R_free r_free	0.2618

CRYSTAL STRUCTURE OF Precorrin-6y C5,15-methyltransferase FROM Geobacter metallireducens GS-15

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

Precorrin-6Y C5,15-methyltransferase (Decarboxylating)

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

3e05__assembly_2__model_1

3e05__assembly_2__model_1 | I(q)

3e05__assembly_2__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF Precorrin-6y C5,15-methyltransferase FROM Geobacter metallireducens GS-15

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

Precorrin-6Y C5,15-methyltransferase (Decarboxylating)

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

3e05__assembly_2__model_1

3e05__assembly_2__model_1 | I(q)

3e05__assembly_2__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)