1lu9

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylobacterium extorquens AM1

Method: X-RAY DIFFRACTION

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

Methylene Tetrahydromethanopterin Dehydrogenase

Methylobacterium extorquens

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTDA_METEX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–287； UniProt 1–287 Author chain B； PDBConstruct 1–287； UniProt 1–287 Author chain C； PDBConstruct 1–287； UniProt 1–287

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	1lu9
Deposition date deposition_date	2002-05-22
Structure title title	Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylobacterium extorquens AM1
Keywords keywords	alpha/beta twisted open sheet structure, Oxidoreductase; 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.

1lu9__assembly_1__model_1

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

Download this curve (.dat)

1lu9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1lu9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.99 Å
Rg (electron density)	32.42 Å
Total Rg	32.94 Å
Atom count	6252
Residues	861
Excluded volume	111280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1lu9__assembly_1__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) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1lu9a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1lu9a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.4 — Methylene-tetrahydromethanopterin dehydrogenase

Domain ID domain_id	d1lu9b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1lu9b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.4 — Methylene-tetrahydromethanopterin dehydrogenase

Domain ID domain_id	d1lu9c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1lu9c2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.4 — Methylene-tetrahydromethanopterin dehydrogenase

CATH v4.4 (6 domains)

Domain ID domain_id	1lu9A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10280 — Methylene-tetrahydromethanopterin dehydrogenase, N-terminal domain

Domain ID domain_id	1lu9A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1lu9B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10280 — Methylene-tetrahydromethanopterin dehydrogenase, N-terminal domain

Domain ID domain_id	1lu9B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1lu9C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10280 — Methylene-tetrahydromethanopterin dehydrogenase, N-terminal domain

Domain ID domain_id	1lu9C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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Unit-cell length a length_a	133.130 Å
Unit-cell length b length_b	85.240 Å
Unit-cell length c length_c	92.370 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.81 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	29.890 Å
R factor r_factor	0.1890
R_work r_work	0.1890
R_free r_free	0.2290

Description description	Methylene Tetrahydromethanopterin Dehydrogenase
Molecular weight formula_weight	29640.6 kDa
EC 编号 ec_number	1.5.1.5
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7803

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylobacterium extorquens AM1

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

Methylene Tetrahydromethanopterin Dehydrogenase

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

1lu9__assembly_1__model_1

1lu9__assembly_1__model_1 | I(q)

1lu9__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)

Source organism organism	Methylobacterium extorquens
NCBI taxonomy ID ncbi_taxonomy_id	272630
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	558

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylobacterium extorquens AM1

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

Methylene Tetrahydromethanopterin Dehydrogenase

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

1lu9__assembly_1__model_1

1lu9__assembly_1__model_1 | I(q)

1lu9__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)