8qml

(2R,4R)-MeTDA bound HydE structure (control experiment)

Method: X-RAY DIFFRACTION

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

[FeFe] hydrogenase maturase subunit HydE

Thermotoga maritima MSB8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	S-ADENOSYL-L-HOMOCYSTEINE × 1 (2R,4R)-2-methyl-1,3-thiazolidine-2,4-dicarboxylic acid × 1 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 5 IRON/SULFUR CLUSTER × 1 CHLORIDE ION × 1 SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HYDE_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–358； UniProt 2–348

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	8qml
Deposition date deposition_date	2023-09-22
Structure title title	(2R,4R)-MeTDA bound HydE structure (control experiment)
Keywords keywords	[FeFe]-hydrogenase, radical SAM enzyme, HydE, Maturase, Complex-B, H-cluster, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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.

8qml__assembly_1__model_1

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

Download this curve (.dat)

8qml__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8qml__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.99 Å
Rg (electron density)	19.34 Å
Total Rg	20.19 Å
Atom count	2935
Residues	345
Excluded volume	53200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8qml__assembly_1__model_1`	monomeric （1）	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	[FeFe] hydrogenase maturase subunit HydE
Molecular weight formula_weight	41025.4 kDa
EC 编号 ec_number	1.8.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3720

MWSHPQFEKASTGREILEKLERREFTREVLKEALSINDRGFNEALFKLADEIRRKYVGDEVHIRAIIEFSNVCRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQSGEDPYXMPDVISDIVKEIKKMGVAVTLSLGEWPREYYEKWKEAGADRYLLRHETANPVLHRKLRPDTSFENRLNCLLTLKELGYETGAGSMVGLPGQTIDDLVDDLLFLKEHDFDMVGIGPFIPHPDTPLANEKKGDFTLTLKMVALTRILLPDSNIPATTAMGTIVPGGREITLRCGANVIMPNWTPSPYRQLYQLYPGKISVFEKDTASIPSVMKMIELLGRKPGRDWGGRKRVFETV

Source Source

Source organism organism	Thermotoga maritima MSB8
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	(2R,4R)-2-methyl-1,3-thiazolidine-2,4-dicarboxylic acid
Molecular weight formula_weight	191.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
Molecular weight formula_weight	614.9 kDa
Source method src_method	syn
Copy count entity_count	5

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	1

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	SULFATE ION
Molecular weight formula_weight	96.1 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	324

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Unit-cell length a length_a	50.480 Å
Unit-cell length b length_b	79.220 Å
Unit-cell length c length_c	85.160 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	23.140 Å
R factor r_factor	0.1559
R_work r_work	0.1540
R_free r_free	0.1925

(2R,4R)-MeTDA bound HydE structure (control experiment)

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

[FeFe] hydrogenase maturase subunit HydE

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

8qml__assembly_1__model_1

8qml__assembly_1__model_1 | I(q)

8qml__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

7. Citations (1)

(2R,4R)-MeTDA bound HydE structure (control experiment)

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

[FeFe] hydrogenase maturase subunit HydE

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

8qml__assembly_1__model_1

8qml__assembly_1__model_1 | I(q)

8qml__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

7. Citations (1)