SAXSdb — 9sc9

▼

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

L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 GLYCEROL × 4 POTASSIUM ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MDH_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–313； UniProt 1–313 Author chain B； PDBConstruct 1–313； UniProt 1–313 Author chain C； PDBConstruct 1–313； UniProt 1–313 Author chain D； PDBConstruct 1–313； UniProt 1–313

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	9sc9
Deposition date deposition_date	2025-08-09
Structure title title	Crystal structure of Methanocaldococcus jannaschii Malate dehydrogenase C7GP mutant
Keywords keywords	Malate dehydrogenase, NADP binding domain, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

9sc9__assembly_1__model_1

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

Download this curve (.dat)

9sc9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9sc9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.04 Å
Rg (electron density)	30.78 Å
Total Rg	31.51 Å
Atom count	19569
Residues	1242
Excluded volume	174270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9sc9__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
Molecular weight formula_weight	35054.6 kDa
EC 编号 ec_number	1.1.1.375
Mutation mutation	P24S, E42K, E46M, R56G, P85A, K105N, D135E, K137G, R140K, K198R, T216G, K217Y, E219K, R223D, D266G, R277K, D289N, A295G, K305G
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	19569

MKVTIIGASGRVGSATALLLAKESFMKDLVLIGREHSINKLKGLRMDIYDALAGTGSDANIYVESDENLRIIDESDVVIITSGVARKEGMSRMDLAKTNAKIVGNYAKKIAEICDTKIFVITNPVDVMTYKALVESGFEKNQVFGLGTHLDSLRFKVAIAKFFGVHIDEVRTRIIGEHGDSMVPLLSATSIGGIPIQRFERFKELPIDEIIEDVKGYGKQIIDLKGGSEFGPAAAILNVVRCIVNNEKRLLTLSAYVDGEFDGIRGVCIGVPVKIGKDGIEEVVSIELNKDEIIGFRKSAEIIKGYCEEVKNLHHHHHH

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	745.4 kDa
Source method src_method	syn
Copy count entity_count	4

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	4

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	4

▶

Unit-cell length a length_a	73.992 Å
Unit-cell length b length_b	75.534 Å
Unit-cell length c length_c	118.502 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.57 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	117.940 Å
R factor r_factor	0.2068
R_work r_work	0.2049
R_free r_free	0.2458

Crystal structure of Methanocaldococcus jannaschii Malate dehydrogenase C7GP mutant

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

L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))

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

9sc9__assembly_1__model_1

9sc9__assembly_1__model_1 | I(q)

9sc9__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 (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 non-polymer

7. Citations (1)

Crystal structure of Methanocaldococcus jannaschii Malate dehydrogenase C7GP mutant

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

L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))

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

9sc9__assembly_1__model_1

9sc9__assembly_1__model_1 | I(q)

9sc9__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 (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 non-polymer

7. Citations (1)