SAXSdb — 9xax

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

SDR family NAD(P)-dependent oxidoreductase

Paracoccus litorisediminis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–244 Chain F； UniProt 2–244 Chain I； UniProt 2–244 Chain J； UniProt 2–244	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 TTN TARTRONATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；293 K；25% w/v PEG 3350, 0.1M Tris pH 8.5	Resolution 2.08 Å R-free 0.201
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 2–244 Chain E； UniProt 2–244 Chain G； UniProt 2–244 Chain K； UniProt 2–244	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 TTN TARTRONATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；293 K；25% w/v PEG 3350, 0.1M Tris pH 8.5	Resolution 2.08 Å R-free 0.201
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 2–244 Chain D； UniProt 2–244 Chain H； UniProt 2–244 Chain L； UniProt 2–244	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 TTN TARTRONATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；293 K；25% w/v PEG 3350, 0.1M Tris pH 8.5	Resolution 2.08 Å R-free 0.201

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9XAX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9X6I Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (ligand-free form) Deposited 2025-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–244（243 aa） Chain B 2–244（243 aa） Chain E 2–244（243 aa） Chain F 2–244（243 aa）	Not recorded	SO4 SULFATE ION × 4 GOL GLYCEROL × 11 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.2M Lithium sulfate monohydrate, 0.1M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350	Resolution 1.90 Å R-free 0.199
9X6I Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (ligand-free form) Deposited 2025-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 2–244（243 aa） Chain G 2–244（243 aa） Chain I 2–244（243 aa） Chain J 2–244（243 aa）	Not recorded	SO4 SULFATE ION × 4 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.2M Lithium sulfate monohydrate, 0.1M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350	Resolution 1.90 Å R-free 0.199
9X6I Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (ligand-free form) Deposited 2025-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain D 2–244（243 aa） Chain H 2–244（243 aa） Chain K 2–244（243 aa） Chain L 2–244（243 aa）	Not recorded	SO4 SULFATE ION × 4 GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.2M Lithium sulfate monohydrate, 0.1M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350	Resolution 1.90 Å R-free 0.199

1 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A844HLS7_9RHOB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–255； UniProt 2–244 Author chain B； PDBConstruct 13–255； UniProt 2–244 Author chain C； PDBConstruct 13–255； UniProt 2–244 Author chain D； PDBConstruct 13–255； UniProt 2–244 Author chain E； PDBConstruct 13–255； UniProt 2–244 Author chain F； PDBConstruct 13–255； UniProt 2–244 Author chain G； PDBConstruct 13–255； UniProt 2–244 Author chain H； PDBConstruct 13–255； UniProt 2–244 Author chain I； PDBConstruct 13–255； UniProt 2–244 Author chain J； PDBConstruct 13–255； UniProt 2–244 Author chain K； PDBConstruct 13–255； UniProt 2–244 Author chain L； PDBConstruct 13–255； UniProt 2–244

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	9xax
Deposition date deposition_date	2025-10-23
Structure title title	Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (NADP+ and tartronate bound form)
Keywords keywords	Short chain dihydrogenase/reductase superfamily, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	49.84 Å
Radius of gyration Rg (electron density) rg_electron	49.85 Å
Forward intensity I(0) i0	1527450000.00
Molecular weight molecular_weight	308060.0 kDa
Excluded volume excluded_volume	378590 Å³
Envelope volume envelope_volume	518410 Å³
Hydration-shell volume shell_volume	87700 Å³
Envelope diameter envelope_diameter	177.9 Å
Shell Rg shell_rg	53.08 Å
Envelope Rg envelope_rg	49.00 Å
Shape Rg shape_rg	49.86 Å
Total Rg total_rg	49.92 Å
Total atoms total_atoms	21564
Residues n_residues	2833
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	172.8 Å
Rg (real space) rg_real	49.94 Å
Rg uncertainty (real space) rg_real_error	1.96 Å
I(0) (real space) i0_real	1.5270e+09
I(0) uncertainty (real space) i0_real_error	2.8200e+07
Rg (reciprocal space) rg_reciprocal	49.84 Å
I(0) (reciprocal space) i0_reciprocal	1527000000.0000
Solution quality estimate total_estimate	0.8592
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	59.4 Å
Skewness Skewness skewness	0.411
Kurtosis Kurtosis kurtosis	-0.205
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	86430000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.808

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	SDR family NAD(P)-dependent oxidoreductase
Molecular weight formula_weight	27366.1 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	23163

MRGSHHHHHHGSKNILITGGGSGVGRATARRFLIEGWQVGLIGRREDALQETAEDNPNALILPCDVTDEAAVDATFAKVASSWGRLDILFNNAGAVLPSTLIDEITVADWRRVTDVNITGMFLCARAAFRQMRNQQPMGGRIINNGSISADVPRPGSVPYTVSKHAVTGLTRTLSLDGRPFNIACGQVDIGNALTDMAVAMTKGVPQADGSTKIEPVIDVKTVADSVWHMATMPEGANIQWLTVMATNMPYIGRG

来源 Source

来源生物 organism	Paracoccus litorisediminis
NCBI Class编号 ncbi_taxonomy_id	2006130
宿主生物 host_organism	Escherichia coli DH5[alpha]

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	12

Entity 3 Entity 3 non-polymer

Description description	TARTRONATE
Molecular weight formula_weight	118.0 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1599

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8. Citations (1)

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Unit-cell length a length_a	69.359 Å
Unit-cell length b length_b	72.552 Å
Unit-cell length c length_c	140.251 Å
Unit-cell angle α angle_alpha	85.28 °
Unit-cell angle β angle_beta	82.57 °
Unit-cell angle γ angle_gamma	84.52 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	48.290 Å
R factor r_factor	0.1703
R_work r_work	0.1686
R_free r_free	0.2007

fit	/app/data/saxs_computation/xa/9xax/9xax.fit
pddf	/app/data/pr_computation/xa/9xax/9xax.pr.out
profile	/app/data/saxs_computation/xa/9xax/9xax.dat

Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (NADP+ and tartronate bound form)

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

SDR family NAD(P)-dependent oxidoreductase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction