SAXSdb — 9r76

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

6-phosphogluconate dehydrogenase NAD-binding protein

Kribbella flavida

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 SULFATE ION × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D2PR38_KRIFD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–296； UniProt 1–296 Author chain B； PDBConstruct 1–296； UniProt 1–296

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	9r76
Deposition date deposition_date	2025-05-14
Last revision last_revision	2025-11-05
Structure title title	Imine Reductase IR91 from Kribbella flavida with NADP+
Keywords keywords	Amine, Imine, NADPH, Imine Reductase, 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.

9r76__assembly_1__model_1

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

Download this curve (.dat)

9r76__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9r76__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.24 Å
Rg (electron density)	26.77 Å
Total Rg	27.20 Å
Atom count	4264
Residues	574
Excluded volume	75308 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9r76__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 (4)

Entity 1 Entity 1 polymer

Description description	6-phosphogluconate dehydrogenase NAD-binding protein
Molecular weight formula_weight	30880.9 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	4635

MPPTDRTPVTLIGLGPMGQAMTRALLAAGHPVTVWNRTPARAAGVVADGAVLAASPVEAVEAGDLVILSLTDYQAMYDVLEPATGSLAGRTVVNLSSDTPDRTRAAADWATEHGATFLTGGVMIPAPMVGTEEAYVYYSGPAEVFEKHRTTLTVIGAPRYLGEDTGLAQLMYQAQLDVFLTTLSSLMHATALLGTAGVSAAESMPELIGMLRTVPAMLEAGGENPGADIDADKHPGDLSTITMMGATADHIVGASETAGIDLALPRAVQAHYRRAIENGHGGDNWTRIIDGIRSPR

Source Source

Source organism organism	Kribbella flavida
NCBI taxonomy ID ncbi_taxonomy_id	182640
Host organism host_organism	Escherichia coli

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	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	357

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Unit-cell length a length_a	52.020 Å
Unit-cell length b length_b	109.430 Å
Unit-cell length c length_c	53.720 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.94 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.490 Å
Low-resolution limit resolution_low	54.720 Å
R factor r_factor	0.2329
R_work r_work	0.2319
R_free r_free	0.2526

Imine Reductase IR91 from Kribbella flavida with NADP+

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

6-phosphogluconate dehydrogenase NAD-binding protein

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

9r76__assembly_1__model_1

9r76__assembly_1__model_1 | I(q)

9r76__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 water

7. Citations (1)

Imine Reductase IR91 from Kribbella flavida with NADP+

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

6-phosphogluconate dehydrogenase NAD-binding protein

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

9r76__assembly_1__model_1

9r76__assembly_1__model_1 | I(q)

9r76__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 water

7. Citations (1)