SAXSdb — 2g8y

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

Malate/L-lactate dehydrogenases

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 8 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 1,2-ETHANEDIOL × 10 PENTAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YBIC_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–383； UniProt 1–361 Author chain B； PDBConstruct 23–383； UniProt 1–361

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	2g8y
Deposition date deposition_date	2006-03-03
Structure title title	The structure of a putative malate/lactate dehydrogenase from E. coli.
Keywords keywords	;malate, lactate, dehydrogenase, NAD, E.coli, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, 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.

2g8y__assembly_1__model_1

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

Download this curve (.dat)

2g8y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2g8y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.16 Å
Rg (electron density)	26.29 Å
Total Rg	26.93 Å
Atom count	5622
Residues	701
Excluded volume	98970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2g8y__assembly_1__model_1`	dimeric （2）	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 (6)

Entity 1 Entity 1 polymer

Description description	Malate/L-lactate dehydrogenases
Molecular weight formula_weight	42158.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6576

MGSSHHHHHHSSGRENLYFQGHMESGHRFDAQTLHSFIQAVFRQMGSEEQEAKLVADHLIAANLAGHDSHGIGMFPSYVRSWSQGHLQINHHAKTVKEAGAAVTLDGDRAFGQVAAHEAMALGIEKAHQHGIAAVALHNSHHIGRIGYWAEQCAAAGFVSIHFVSVVGIPMVAPFHGRDSRFGTNPFCVVFPRKDNFPLLLDYATSAIAFGKTRVAWHKGVPVPPGCLIDVNGVPTTNPAVMQESPLGSLLTFAEHKGYALAAMCEILGGALSGGKTTHQETLQTSPDAILNCMTTIIINPELFGAPDCNAQTEAFAEWVKASPHDDDKPILLPGEWEVNTRRERQKQGIPLDAGSWQAICDAARQIGMPEETLQAFCQQLASGS

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	877

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2g8ya_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.122 — L-sulfolactate dehydrogenase-like
Superfamily Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
Family Family family	c.122.1.0 — automated matches

Domain ID domain_id	d2g8yb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.122 — L-sulfolactate dehydrogenase-like
Superfamily Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
Family Family family	c.122.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	2g8yA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

Domain ID domain_id	2g8yA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

Domain ID domain_id	2g8yA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	460 — Single helix bin

Domain ID domain_id	2g8yB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

Domain ID domain_id	2g8yB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

Domain ID domain_id	2g8yB03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	460 — Single helix bin

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Unit-cell length a length_a	139.095 Å
Unit-cell length b length_b	139.095 Å
Unit-cell length c length_c	151.654 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	35.500 Å
R factor r_factor	0.1590
R_work r_work	0.1576
R_free r_free	0.1862

The structure of a putative malate/lactate dehydrogenase from E. coli.

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

Malate/L-lactate dehydrogenases

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

2g8y__assembly_1__model_1

2g8y__assembly_1__model_1 | I(q)

2g8y__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)

The structure of a putative malate/lactate dehydrogenase from E. coli.

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

Malate/L-lactate dehydrogenases

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

2g8y__assembly_1__model_1

2g8y__assembly_1__model_1 | I(q)

2g8y__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)