6tlk

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT

Method: X-RAY DIFFRACTION

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

Bifunctional protein MdtA

Methylorubrum extorquens AM1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 3 FORMIC ACID × 4 5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN × 2 GLYCEROL × 2 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 3 FORMIC ACID × 9 GLYCEROL × 4 CHLORIDE ION × 1 MAGNESIUM ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTDA_METEA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–288； UniProt 1–288 Author chain B； PDBConstruct 1–288； UniProt 1–288 Author chain C； PDBConstruct 1–288； UniProt 1–288 Author chain D； PDBConstruct 1–288； UniProt 1–288 Author chain E； PDBConstruct 1–288； UniProt 1–288 Author chain F； PDBConstruct 1–288； UniProt 1–288

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	6tlk
Deposition date deposition_date	2019-12-02
Structure title title	Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT
Keywords keywords	One-carbon metabolism; Enzyme catalysis; Dehydrogenase; Conformational changes; Methylotrophy, 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.

6tlk__assembly_1__model_1

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

Download this curve (.dat)

6tlk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6tlk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.24 Å
Rg (electron density)	32.74 Å
Total Rg	33.20 Å
Atom count	6522
Residues	865
Excluded volume	115560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6tlk__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6tlk__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Description description	Bifunctional protein MdtA
Molecular weight formula_weight	31512.7 kDa
EC 编号 ec_number	1.5.1.-,1.5.1.5
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	15166

MSKKLLFQFDTDATPSVFDVVVGYDGGADHITGYGNVTPDNVGAYVDGTIYTRGGKEKQSTAIFVGGGDMAAGERVFEAVKKRFFGPFRVSCMLDSNGSNTTAAAGVALVVKAAGGSVKGKKAVVLAGTGPVGMRSAALLAGEGAEVVLCGRKLDKAQAAADSVNKRFKVNVTAAETADDASRAEAVKGAHFVFTAGAIGLELLPQAAWQNESSIEIVADYNAQPPLGIGGIDATDKGKEYGGKRAFGALGIGGLKLKLHRACIAKLFESSEGVFDAEEIYKLAKEMAVDKLAAALEHHHHHH

Source Source

Source organism organism	Methylorubrum extorquens AM1
NCBI taxonomy ID ncbi_taxonomy_id	272630
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	743.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 4 Entity 4 non-polymer

Description description	5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN
Molecular weight formula_weight	788.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	nat
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2093

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	6tlkA01
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	6tlkA02
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	6tlkB01
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	6tlkB02
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	6tlkC01
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	6tlkC02
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	6tlkD01
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	6tlkD02
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	6tlkE01
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	6tlkE02
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	6tlkF01
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	6tlkF02
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	76.923 Å
Unit-cell length b length_b	149.267 Å
Unit-cell length c length_c	78.559 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.64 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	26.350 Å
R factor r_factor	0.1670
R_work r_work	0.1660
R_free r_free	0.2010

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT

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

Bifunctional protein MdtA

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

6tlk__assembly_1__model_1

6tlk__assembly_1__model_1 | I(q)

6tlk__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 non-polymer

Entity 3 Entity 3 non-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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT

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

Bifunctional protein MdtA

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

6tlk__assembly_1__model_1

6tlk__assembly_1__model_1 | I(q)

6tlk__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 non-polymer

Entity 3 Entity 3 non-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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)