SAXSdb — 3dms

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

Isocitrate dehydrogenase [NADP]

Burkholderia pseudomallei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q63WJ4_BURPS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–427； UniProt 1–419

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	3dms
Deposition date deposition_date	2008-07-01
Structure title title	1.65A crystal structure of isocitrate dehydrogenase from Burkholderia pseudomallei
Keywords keywords	;BURKHOLDERIA, PSEUDOMALLEI, ISOCITRATE, DEHYDROGENASE, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, SSGCID, Glyoxylate bypass, Manganese, Metal-binding, NADP, Oxidoreductase, Tricarboxylic acid cycle ;; 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.

3dms__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3dms__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dms__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	23.66 Å
Rg (electron density)	22.66 Å
Total Rg	23.57 Å
Atom count	3211
Residues	413
Excluded volume	57673 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dms__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dms__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Description description	Isocitrate dehydrogenase [NADP]
Molecular weight formula_weight	47231.1 kDa
EC 编号 ec_number	1.1.1.42
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	3537

MAHHHHHHMPYQHIKVPEGGDKITVNKDFSLNVSDQPIIPYIEGDGTGFDITPVMIKVVDAAVEKAYGGKKKIHWMEIYAGEKATKVYGPDVWLPEETLQVLKEYVVSIKGPLTTPVGGGIRSLNVALRQELDLYVCLRPIQYFKGVPSPVREPEKTNMVIFRENSEDIYAGIEWAAESEQAKKVIKFLQEEMGVKKIRFPQTSGIGIKPVSKEGTERLVRKAIQYAIDNDRKSVTLVHKGNIMKFTEGAFRDAGYALAQKEFGAELIDGGPWMKFKNPKTGNEIVVKDSIADAFLQQILLRPAEYDVIATLNLNGDYISDALAAQVGGIGIAPGANLSDSVAMFEATHGTAPKYAGKDYVNPGSEILSAEMMLRHLGWTEAADVIISAMEKSIKQKRVTYDFARLMEGATQVSCSGFGQVLIENME

Source Source

Source organism organism	Burkholderia pseudomallei
Common name common_name	Pseudomonas pseudomallei
NCBI taxonomy ID ncbi_taxonomy_id	28450
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	262

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3dmsa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
Family Family family	c.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

CATH v4.4 (1 domains)

Domain ID domain_id	3dmsA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	718 — Isopropylmalate Dehydrogenase
Homologous superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

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Unit-cell length a length_a	103.993 Å
Unit-cell length b length_b	62.238 Å
Unit-cell length c length_c	70.998 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.52 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	45.690 Å
R factor r_factor	0.2060
R_work r_work	0.2050
R_free r_free	0.2340

1.65A crystal structure of isocitrate dehydrogenase from Burkholderia pseudomallei

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

Isocitrate dehydrogenase [NADP]

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

3dms__assembly_2__model_1

3dms__assembly_2__model_1 | I(q)

3dms__assembly_2__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (2)

1.65A crystal structure of isocitrate dehydrogenase from Burkholderia pseudomallei

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

Isocitrate dehydrogenase [NADP]

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

3dms__assembly_2__model_1

3dms__assembly_2__model_1 | I(q)

3dms__assembly_2__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (2)